list configuration is excessive

Having some questions:

- Is it the first time you're using grub customizer on this system?
- Are the duplicates on your boot screen too?
- What's the output of `ls -Rl /etc/grub.d`?

ken@Z68:~$ ls -Rl /etc/grub.d
/etc/grub.d:
total 56
-rwxr-xr-x 1 root root 7806 Jun 26 03:58 00_header.dpkg-dist
-rwxr-xr-x 1 root root 739 Dec 1 13:20 10_linux_proxy
-rwxr-xr-x 1 root root 210 Dec 1 13:20 30_os-prober_proxy
-rwxr-xr-x 1 root root 739 Dec 1 13:20 31_linux_proxy
-rwxr-xr-x 1 root root 7806 Jul 25 2014 33_header
-rwxr-xr-x 1 root root 5522 Jul 25 2014 34_debian_theme
-rwxr-xr-x 1 root root 265 Dec 1 13:20 39_memtest86+_proxy
drwxr-xr-x 4 root root 4096 Jul 12 2014 backup
drwxr-xr-x 2 root root 4096 Jul 12 2014 bin
drwxr-xr-x 2 root root 4096 Dec 1 13:20 proxifiedScripts
-rw-r--r-- 1 root root 483 Jul 25 2014 README

/etc/grub.d/backup:
total 24
drwxr-xr-x 3 root root 12288 Jul 12 2014 boot_grub
-rw-r--r-- 1 root root 1238 Jul 12 2014 default_grub
drwxr-xr-x 2 root root 4096 Jul 12 2014 etc_grub_d
-rw-r--r-- 1 root root 519 Jul 12 2014 RESTORE_INSTRUCTIONS

/etc/grub.d/backup/boot_grub:
total 4352
-rw-r--r-- 1 root root 7368 Jul 12 2014 915resolution.mod
-rw-r--r-- 1 root root 10420 Jul 12 2014 acpi.mod
-rw-r--r-- 1 root root 1848 Jul 12 2014 adler32.mod
-rw-r--r-- 1 root root 4644 Jul 12 2014 affs.mod
-rw-r--r-- 1 root root 5092 Jul 12 2014 afs_be.mod
-rw-r--r-- 1 root root 4928 Jul 12 2014 afs.mod
-rw-r--r-- 1 root root 1132 Jul 12 2014 aout.mod
-rw-r--r-- 1 root root 8184 Jul 12 2014 ata.mod
-rw-r--r-- 1 root root 2276 Jul 12 2014 ata_pthru.mod
-rw-r--r-- 1 root root 4236 Jul 12 2014 at_keyboard.mod
-rw-r--r-- 1 root root 5004 Jul 12 2014 befs_be.mod
-rw-r--r-- 1 root root 4832 Jul 12 2014 befs.mod
-rw-r--r-- 1 root root 4780 Jul 12 2014 biosdisk.mod
-rw-r--r-- 1 root root 2560 Jul 12 2014 bitmap.mod
-rw-r--r-- 1 root root 3084 Jul 12 2014 bitmap_scale.mod
-rw-r--r-- 1 root root 2192 Jul 12 2014 blocklist.mod
-rw-r--r-- 1 root root 512 Jul 12 2014 boot.img
-rw-r--r-- 1 root root 2636 Jul 12 2014 boot.mod
-rw-r--r-- 1 root root 27992 Jul 12 2014 bsd.mod
-rw-r--r-- 1 root root 13588 Jul 12 2014 btrfs.mod
-rw-r--r-- 1 root root 2032 Jul 12 2014 bufio.mod
-rw-r--r-- 1 root root 2428 Jul 12 2014 cat.mod
-rw-r--r-- 1 root root 512 Jul 12 2014 cdboot.img
-rw-r--r-- 1 root root 2652 Jul 12 2014 chain.mod
-rw-r--r-- 1 root root 1720 Jul 12 2014 cmostest.mod
-rw-r--r-- 1 root root 2136 Jul 12 2014 cmp.mod
-rw-r--r-- 1 root root 2830 Jul 12 2014 command.lst
-rw-r--r-- 1 root root 2368 Jul 12 2014 configfile.mod
-rw-r--r-- 1 root root 26099 Jul 12 2014 core.img
-rw-r--r-- 1 root root 2940 Jul 12 2014 cpio.mod
-rw-r--r-- 1 root root 1684 Jul 12 2014 cpuid.mod
-rw-r--r-- 1 root root 842 Jul 12 2014 crypto.lst
-rw-r--r-- 1 root root 4464 Jul 12 2014 crypto.mod
-rw-r--r-- 1 root root 4212 Jul 12 2014 cs5536.mod
-rw-r--r-- 1 root root 1952 Jul 12 2014 datehook.mod
-rw-r--r-- 1 root root 2336 Jul 12 2014 date.mod
-rw-r--r-- 1 root root 1353 Jul 12 2014 datetime.mod
-rw-r--r-- 1 root root 512 Jul 12 2014 diskboot.img
-rw-r--r-- 1 root root 1968 Jul 12 2014 dm_nv.mod
-rw-r--r-- 1 root root 5576 Jul 12 2014 drivemap.mod
-rw-r--r-- 1 root root 2108 Jul 12 2014 echo.mod
-rw-r--r-- 1 root root 7408 Jul 12 2014 efiemu32.o
-rw-r--r-- 1 root root 11089 Jul 12 2014 efiemu64.o
-rw-r--r-- 1 root root 24580 Jul 12 2014 efiemu.mod
-rw-r--r-- 1 root root 4632 Jul 12 2014 elf.mod
-rw-r--r-- 1 root root 1700 Jul 12 2014 example_functional_test.mod
-rw-r--r-- 1 root root 5912 Jul 12 2014 ext2.mod
-rw-r--r-- 1 root root 4572 Jul 12 2014 extcmd.mod
-rw-r--r-- 1 root root 6100 Jul 12 2014 fat.mod
-rw-r--r-- 1 root root 11976 Jul 12 2014 font.mod
-rw-r--r-- 1 root root 2892 Jul 12 2014 fshelp.mod
-rw-r--r-- 1 root root 149 Jul 12 2014 fs.lst
-rw-r--r-- 1 root root 2556 Jul 12 2014 functional_test.mod
-rw-r--r-- 1 root root 512 Jul 12 2014 g2hdr.img
-rw-r--r-- 1 root root 1824 Jul 12 2014 gcry_arcfour.mod
-rw-r--r-- 1 root root 8308 Jul 12 2014 gcry_blowfish.mod
-rw-r--r-- 1 root root 34668 Jul 12 2014 gcry_camellia.mod
-rw-r--r-- 1 root root 17412 Jul 12 2014 gcry_cast5.mod
-rw-r--r-- 1 root root 3088 Jul 12 2014 gcry_crc.mod
-rw-r--r-- 1 root root 19440 Jul 12 2014 gcry_des.mod
-rw-r--r-- 1 root root 3304 Jul 12 2014 gcry_md4.mod
-rw-r--r-- 1 root root 3988 Jul 12 2014 gcry_md5.mod
-rw-r--r-- 1 root root 2632 Jul 12 2014 gcry_rfc2268.mod
-rw-r--r-- 1 root root 19236 Jul 12 2014 gcry_rijndael.mod
-rw-r--r-- 1 root root 8752 Jul 12 2014 gcry_rmd160.mod
-rw-r--r-- 1 root root 16740 Jul 12 2014 gcry_seed.mod
-rw-r--r-- 1 root root 18092 Jul 12 2014 gcry_serpent.mod
-rw-r--r-- 1 root root 8856 Jul 12 2014 gcry_sha1.mod
-rw-r--r-- 1 root root 3660 Jul 12 2014 gcry_sha256.mod
-rw-r--r-- 1 root root 5868 Jul 12 2014 gcry_sha512.mod
-rw-r--r-- 1 root root 11916 Jul 12 2014 gcry_tiger.mod
-rw-r--r-- 1 root root 39688 Jul 12 2014 gcry_twofish.mod
-rw-r--r-- 1 root root 24712 Jul 12 2014 gcry_whirlpool.mod
-rw-r--r-- 1 root root 4012 Jul 12 2014 gettext.mod
-rw-r--r-- 1 root root 699 Jul 12 2014 gfxblacklist.txt
-rw-r--r-- 1 root root 32992 Jul 12 2014 gfxmenu.mod
-rw-r--r-- 1 root root 11996 Jul 12 2014 gfxterm.mod
-rw-r--r-- 1 root root 3780 Jul 12 2014 gptsync.mod
-rw-r--r-- 1 root root 10240 Jul 12 2014 grldr.img
-rw-r--r-- 1 root root 5681 Jul 12 2014 grub.cfg
-rw-r--r-- 1 root root 1024 Jul 12 2014 grubenv
-rw-r--r-- 1 root root 8704 Jul 12 2014 gzio.mod
-rw-r--r-- 1 root root 4076 Jul 12 2014 halt.mod
-rw-r--r-- 1 root root 5136 Jul 12 2014 hashsum.mod
-rw-r--r-- 1 root root 7404 Jul 12 2014 hdparm.mod
-rw-r--r-- 1 root root 1292 Jul 12 2014 hello.mod
-rw-r--r-- 1 root root 2548 Jul 12 2014 help.mod
-rw-r--r-- 1 root root 3296 Jul 12 2014 hexdump.mod
-rw-r--r-- 1 root root 6136 Jul 12 2014 hfs.mod
-rw-r--r-- 1 root root 6024 Jul 12 2014 hfsplus.mod
-rw-r--r-- 1 root root 38972 Jul 12 2014 hwmatch.mod
-rw-r--r-- 1 root root 2928 Jul 12 2014 iorw.mod
-rw-r--r-- 1 root root 6344 Jul 12 2014 iso9660.mod
-rw-r--r-- 1 root root 6212 Jul 12 2014 jfs.mod
-rw-r--r-- 1 root root 5908 Jul 12 2014 jpeg.mod
-rw-r--r-- 1 root root 30312 Jul 12 2014 kernel.img
-rw-r--r-- 1 root root 4588 Jul 12 2014 keylayouts.mod
-rw-r--r-- 1 root root 2104 Jul 12 2014 keystatus.mod
-rw-r--r-- 1 root root 27668 Jul 12 2014 legacycfg.mod
-rw-r--r-- 1 root root 5768 Jul 12 2014 linux16.mod
-rw-r--r-- 1 root root 10180 Jul 12 2014 linux.mod
-rw-r--r-- 1 root root 1024 Jul 12 2014 lnxboot.img
-rw-r--r-- 1 root root 5756 Jul 12 2014 loadenv.mod
drwxr-xr-x 2 root root 4096 Jul 12 2014 locale
-rw-r--r-- 1 root root 2988 Jul 12 2014 loopback.mod
-rw-r--r-- 1 root root 3716 Jul 12 2014 lsacpi.mod
-rw-r--r-- 1 root root 2308 Jul 12 2014 lsapm.mod
-rw-r--r-- 1 root root 1804 Jul 12 2014 lsmmap.mod
-rw-r--r-- 1 root root 4436 Jul 12 2014 ls.mod
-rw-r--r-- 1 root root 4968 Jul 12 2014 lspci.mod
-rw-r--r-- 1 root root 7216 Jul 12 2014 lvm.mod
-rw-r--r-- 1 root root 9084 Jul 12 2014 lzopio.mod
-rw-r--r-- 1 root root 1976 Jul 12 2014 mdraid09.mod
-rw-r--r-- 1 root root 2380 Jul 12 2014 mdraid1x.mod
-rw-r--r-- 1 root root 2144 Jul 12 2014 memdisk.mod
-rw-r--r-- 1 root root 2948 Jul 12 2014 memrw.mod
-rw-r--r-- 1 root root 3528 Jul 12 2014 minicmd.mod
-rw-r--r-- 1 root root 3880 Jul 12 2014 minix2.mod
-rw-r--r-- 1 root root 3880 Jul 12 2014 minix.mod
-rw-r--r-- 1 root root 9300 Jul 12 2014 mmap.mod
-rw-r--r-- 1 root root 3292 Jul 12 2014 moddep.lst
-rw-r--r-- 1 root root 2492 Jul 12 2014 msdospart.mod
-rw-r--r-- 1 root root 12988 Jul 12 2014 multiboot2.mod
-rw-r--r-- 1 root root 12292 Jul 12 2014 multiboot.mod
-rw-r--r-- 1 root root 6716 Jul 12 2014 nilfs2.mod
-rw-r--r-- 1 root root 107476 Jul 12 2014 normal.mod
-rw-r--r-- 1 root root 3540 Jul 12 2014 ntfscomp.mod
-rw-r--r-- 1 root root 9612 Jul 12 2014 ntfs.mod
-rw-r--r-- 1 root root 2636 Jul 12 2014 ntldr.mod
-rw-r--r-- 1 root root 10432 Jul 12 2014 ohci.mod
-rw-r--r-- 1 root root 1772 Jul 12 2014 part_acorn.mod
-rw-r--r-- 1 root root 1856 Jul 12 2014 part_amiga.mod
-rw-r--r-- 1 root root 2192 Jul 12 2014 part_apple.mod
-rw-r--r-- 1 root root 2860 Jul 12 2014 part_bsd.mod
-rw-r--r-- 1 root root 2452 Jul 12 2014 part_gpt.mod
-rw-r--r-- 1 root root 82 Jul 12 2014 partmap.lst
-rw-r--r-- 1 root root 2388 Jul 12 2014 part_msdos.mod
-rw-r--r-- 1 root root 1644 Jul 12 2014 part_sun.mod
-rw-r--r-- 1 root root 1776 Jul 12 2014 part_sunpc.mod
-rw-r--r-- 1 root root 17 Jul 12 2014 parttool.lst
-rw-r--r-- 1 root root 4568 Jul 12 2014 parttool.mod
-rw-r--r-- 1 root root 2052 Jul 12 2014 password.mod
-rw-r--r-- 1 root root 2940 Jul 12 2014 password_pbkdf2.mod
-rw-r--r-- 1 root root 1416 Jul 12 2014 pbkdf2.mod
-rw-r--r-- 1 root root 1272 Jul 12 2014 pci.mod
-rw-r--r-- 1 root root 2568 Jul 12 2014 play.mod
-rw-r--r-- 1 root root 6620 Jul 12 2014 png.mod
-rw-r--r-- 1 root root 2740 Jul 12 2014 probe.mod
-rw-r--r-- 1 root root 1024 Jul 12 2014 pxeboot.img
-rw-r--r-- 1 root root 1408 Jul 12 2014 pxecmd.mod
-rw-r--r-- 1 root root 6160 Jul 12 2014 pxe.mod
-rw-r--r-- 1 root root 1472 Jul 12 2014 raid5rec.mod
-rw-r--r-- 1 root root 2876 Jul 12 2014 raid6rec.mod
-rw-r--r-- 1 root root 6536 Jul 12 2014 raid.mod
-rw-r--r-- 1 root root 1640 Jul 12 2014 read.mod
-rw-r--r-- 1 root root 1200 Jul 12 2014 reboot.mod
-rw-r--r-- 1 root root 41940 Jul 12 2014 regexp.mod
-rw-r--r-- 1 root root 9544 Jul 12 2014 reiserfs.mod
-rw-r--r-- 1 root root 14644 Jul 12 2014 relocator.mod
-rw-r--r-- 1 root root 4028 Jul 12 2014 scsi.mod
-rw-r--r-- 1 root root 2980 Jul 12 2014 search_fs_file.mod
-rw-r--r-- 1 root root 3008 Jul 12 2014 search_fs_uuid.mod
-rw-r--r-- 1 root root 2912 Jul 12 2014 search_label.mod
-rw-r--r-- 1 root root 2628 Jul 12 2014 search.mod
-rw-r--r-- 1 root root 7260 Jul 12 2014 sendkey.mod
-rw-r--r-- 1 root root 7120 Jul 12 2014 serial.mod
-rw-r--r-- 1 root root 706 Jul 12 2014 setjmp.mod
-rw-r--r-- 1 root root 5512 Jul 12 2014 setpci.mod
-rw-r--r-- 1 root root 4052 Jul 12 2014 sfs.mod
-rw-r--r-- 1 root root 2392 Jul 12 2014 sleep.mod
-rw-r--r-- 1 root root 3972 Jul 12 2014 squash4.mod
-rw-r--r-- 1 root root 2968 Jul 12 2014 tar.mod
-rw-r--r-- 1 root root 132 Jul 12 2014 terminal.lst
-rw-r--r-- 1 root root 3836 Jul 12 2014 terminal.mod
-rw-r--r-- 1 root root 10312 Jul 12 2014 terminfo.mod
-rw-r--r-- 1 root root 1508 Jul 12 2014 test_blockarg.mod
-rw-r--r-- 1 root root 2816 Jul 12 2014 testload.mod
-rw-r--r-- 1 root root 5100 Jul 12 2014 test.mod
-rw-r--r-- 1 root root 2940 Jul 12 2014 tga.mod
-rw-r--r-- 1 root root 1763 Jul 12 2014 trig.mod
-rw-r--r-- 1 root root 1356 Jul 12 2014 true.mod
-rw-r--r-- 1 root root 6572 Jul 12 2014 udf.mod
-rw-r--r-- 1 root root 4740 Jul 12 2014 ufs1.mod
-rw-r--r-- 1 root root 5052 Jul 12 2014 ufs2.mod
-rw-r--r-- 1 root root 6004 Jul 12 2014 uhci.mod
-rw-r--r-- 1 root root 2560080 Jul 12 2014 unicode.pf2
-rw-r--r-- 1 root root 4300 Jul 12 2014 usb_keyboard.mod
-rw-r--r-- 1 root root 9656 Jul 12 2014 usb.mod
-rw-r--r-- 1 root root 5604 Jul 12 2014 usbms.mod
-rw-r--r-- 1 root root 2048 Jul 12 2014 usbserial_common.mod
-rw-r--r-- 1 root root 2452 Jul 12 2014 usbserial_ftdi.mod
-rw-r--r-- 1 root root 2812 Jul 12 2014 usbserial_pl2303.mod
-rw-r--r-- 1 root root 3756 Jul 12 2014 usbtest.mod
-rw-r--r-- 1 root root 8840 Jul 12 2014 vbe.mod
-rw-r--r-- 1 root root 4724 Jul 12 2014 vga.mod
-rw-r--r-- 1 root root 2304 Jul 12 2014 vga_text.mod
-rw-r--r-- 1 root root 5536 Jul 12 2014 video_bochs.mod
-rw-r--r-- 1 root root 5860 Jul 12 2014 video_cirrus.mod
-rw-r--r-- 1 root root 19164 Jul 12 2014 video_fb.mod
-rw-r--r-- 1 root root 3748 Jul 12 2014 videoinfo.mod
-rw-r--r-- 1 root root 33 Jul 12 2014 video.lst
-rw-r--r-- 1 root root 10752 Jul 12 2014 video.mod
-rw-r--r-- 1 root root 4268 Jul 12 2014 videotest.mod
-rw-r--r-- 1 root root 6152 Jul 12 2014 xfs.mod
-rw-r--r-- 1 root root 31736 Jul 12 2014 xnu.mod
-rw-r--r-- 1 root root 2016 Jul 12 2014 xnu_uuid.mod
-rw-r--r-- 1 root root 14468 Jul 12 2014 xzio.mod
-rw-r--r-- 1 root root 6360 Jul 12 2014 zfsinfo.mod
-rw-r--r-- 1 root root 33308 Jul 12 2014 zfs.mod

/etc/grub.d/backup/boot_grub/locale:
total 12
-rw-r--r-- 1 root root 937 Jul 12 2014 en_AU.mo
-rw-r--r-- 1 root root 466 Jul 12 2014 en_CA.mo
-rw-r--r-- 1 root root 1862 Jul 12 2014 en_GB.mo

/etc/grub.d/backup/etc_grub_d:
total 60
-rw-r--r-- 1 root root 7806 Jul 12 2014 00_header
-rw-r--r-- 1 root root 5522 Jul 12 2014 05_debian_theme
-rw-r--r-- 1 root root 7877 Jul 12 2014 10_linux
-rw-r--r-- 1 root root 6449 Jul 12 2014 20_linux_xen
-rw-r--r-- 1 root root 1588 Jul 12 2014 20_memtest86+
-rw-r--r-- 1 root root 6675 Jul 12 2014 30_os-prober
-rw-r--r-- 1 root root 1388 Jul 12 2014 30_uefi-firmware
-rw-r--r-- 1 root root 214 Jul 12 2014 40_custom
-rw-r--r-- 1 root root 95 Jul 12 2014 41_custom
-rw-r--r-- 1 root root 483 Jul 12 2014 README

/etc/grub.d/bin:
total 456
-rwxr-xr-x 1 root root 465864 Dec 1 13:20 grubcfg_proxy

/etc/grub.d/proxifiedScripts:
total 48
-rwxr-xr-x 1 root root 214 Jul 25 2014 custom
-rwxr-xr-x 1 root root 95 Jul 25 2014 custom~1
-rwxr-xr-x 1 root root 7877 Jul 25 2014 linux
-rwxr-xr-x 1 root root 7877 Aug 6 2014 linux~
-rwxr-xr-x 1 root root 6449 Jul 25 2014 linux_xen
-rwxr-xr-x 1 root root 1588 Nov 27 2011 memtest86+
-rwxr-xr-x 1 root root 6675 Jul 25 2014 os-prober
-rwxr-xr-x 1 root root 1388 Jul 25 2014 uefi-firmware

- Is it the first time you're using grub customizer on this system?

It's been in use for a while, and had not queried this before, but I reported something else and thought I'd mention it.

- Are the duplicates on your boot screen too?

No, as I deselect the dupicates.

There's a duplicate "header" script. Once with dpkg-dist postfix once without. Don't know why the postfixed one is executable… maybe it came this way from distro. Grub Customizer would put it to proxifiedScripts of not active so the entries wouldn't appear on list.

The other duplicates may also be update problems but I'm wondering why it wasn't detected by grub customizer. New scripts at old positions are treated as updates. I think it will be too hard to replicate this error. Could be caused by manual renaming for example (then the /etc/grub.d/.script_sources.txt which associates the original path with the current path is not updated).

You can fix the problem by removing the duplicate scripts manually:

 /etc/grub.d/proxifiedScripts/linux~
 /etc/grub.d/00_header.dpkg-dist

And then move /etc/grub.d/33_header to /etc/grub.d/00_header as the header always should be the first script.

Then run grub customizer and save the configuration. Make sure the required boot entries are present. Would be bad when your current system isn't there and cannot be booted.

The header.dpkg-dist has disappeared, but everything else is still the same. The Advanced Options for Ubuntu is still not appearing, and it seems that the dual 'linux' sections are separated by the 'os-prober' (for Microssoft Windows XP) so, as before, this at least enables me to have XP as the second item on the list. Not sure that this is easily resolvable, and while I appreciate your response, I don't want it to take up too much of your time.