Windows is missing on reboot

Unless you inserted the windows menuentry manually (in the past) I cannot believe this. Grub customizer doesn't change anything that isn't set by the user.

Please paste your /boot/grub/grub.cfg and the output of "sudo /etc/grub.d/*_os-prober"

Thanks for the quick reply! I suppose I might have done something atypical in the past as this was my first ever install of Linux or windows 10. I never manually altered my grub file (or even knew what grub was till a couple of weeks ago) but I have been tinkering with a lot of things I don't know much about...
I'll post the info you are requesting when I get home in a few hours.

Sorry for my extreme noobishness but I'm trying ;)
Thanks for all your help!

the output of sudo /etc/grub.d/*_os-prober:
No volume groups found

the grub.cfg has this:
#
# DO NOT EDIT THIS FILE
#
# It is automatically generated by grub-mkconfig using templates
# from /etc/grub.d and settings from /etc/default/grub
#

### BEGIN /etc/grub.d/00_header ###
if [ -s $prefix/grubenv ]; then
  set have_grubenv=true
  load_env
fi
if [ "${next_entry}" ] ; then
   set default="${next_entry}"
   set next_entry=
   save_env next_entry
   set boot_once=true
else
   set default="${saved_entry}"
fi

if [ x"${feature_menuentry_id}" = xy ]; then
  menuentry_id_option="--id"
else
  menuentry_id_option=""
fi

export menuentry_id_option

if [ "${prev_saved_entry}" ]; then
  set saved_entry="${prev_saved_entry}"
  save_env saved_entry
  set prev_saved_entry=
  save_env prev_saved_entry
  set boot_once=true
fi

function savedefault {
  if [ -z "${boot_once}" ]; then
    saved_entry="${chosen}"
    save_env saved_entry
  fi
}
function recordfail {
  set recordfail=1
  if [ -n "${have_grubenv}" ]; then if [ -z "${boot_once}" ]; then save_env recordfail; fi; fi
}
function load_video {
  if [ x$feature_all_video_module = xy ]; then
    insmod all_video
  else
    insmod efi_gop
    insmod efi_uga
    insmod ieee1275_fb
    insmod vbe
    insmod vga
    insmod video_bochs
    insmod video_cirrus
  fi
}

if [ x$feature_default_font_path = xy ] ; then
   font=unicode
else
insmod part_msdos
insmod ext2
set root='hd0,msdos2'
if [ x$feature_platform_search_hint = xy ]; then
  search --no-floppy --fs-uuid --set=root --hint-bios=hd0,msdos2 --hint-efi=hd0,msdos2 --hint-baremetal=ahci0,msdos2 b63f2ac6-42d2-48af-beeb-fb001b7c16b2
else
  search --no-floppy --fs-uuid --set=root b63f2ac6-42d2-48af-beeb-fb001b7c16b2
fi
    font="/usr/share/grub/unicode.pf2"
fi

if loadfont $font ; then
  set gfxmode=auto
  load_video
  insmod gfxterm
  set locale_dir=$prefix/locale
  set lang=en_CA
  insmod gettext
fi
terminal_output gfxterm
if [ "${recordfail}" = 1 ] ; then
  set timeout=-1
else
  if [ x$feature_timeout_style = xy ] ; then
    set timeout_style=menu
    set timeout=1
  # Fallback normal timeout code in case the timeout_style feature is
  # unavailable.
  else
    set timeout=1
  fi
fi
### END /etc/grub.d/00_header ###

### BEGIN /etc/grub.d/05_debian_theme ###
set menu_color_normal=white/black
set menu_color_highlight=black/light-gray
### END /etc/grub.d/05_debian_theme ###

### BEGIN /etc/grub.d/06_mint_theme ###
set menu_color_normal=white/black
set menu_color_highlight=white/light-gray
### END /etc/grub.d/06_mint_theme ###

### BEGIN /etc/grub.d/10_linux ###
function gfxmode {
 set gfxpayload="${1}"
 if [ "${1}" = "keep" ]; then
  set vt_handoff=vt.handoff=7
 else
  set vt_handoff=
 fi
}
if [ "${recordfail}" != 1 ]; then
  if [ -e ${prefix}/gfxblacklist.txt ]; then
    if hwmatch ${prefix}/gfxblacklist.txt 3; then
      if [ ${match} = 0 ]; then
        set linux_gfx_mode=keep
      else
        set linux_gfx_mode=text
      fi
    else
      set linux_gfx_mode=text
    fi
  else
    set linux_gfx_mode=keep
  fi
else
  set linux_gfx_mode=text
fi
export linux_gfx_mode
menuentry 'Linux Mint 17.2 Cinnamon 64-bit' --class ubuntu --class gnu-linux --class gnu --class os $menuentry_id_option 'gnulinux-simple-b63f2ac6-42d2-48af-beeb-fb001b7c16b2' {
 recordfail
 savedefault
 load_video
 gfxmode $linux_gfx_mode
 insmod gzio
 insmod part_msdos
 insmod ext2
 set root='hd0,msdos2'
 if [ x$feature_platform_search_hint = xy ]; then
   search --no-floppy --fs-uuid --set=root --hint-bios=hd0,msdos2 --hint-efi=hd0,msdos2 --hint-baremetal=ahci0,msdos2 b63f2ac6-42d2-48af-beeb-fb001b7c16b2
 else
   search --no-floppy --fs-uuid --set=root b63f2ac6-42d2-48af-beeb-fb001b7c16b2
 fi
 linux /boot/vmlinuz-3.16.0-38-generic root=UUID=b63f2ac6-42d2-48af-beeb-fb001b7c16b2 ro persistent profile
 initrd /boot/initrd.img-3.16.0-38-generic
}
submenu 'Advanced options for Linux Mint 17.2 Cinnamon 64-bit' $menuentry_id_option 'gnulinux-advanced-b63f2ac6-42d2-48af-beeb-fb001b7c16b2' {
 menuentry 'Linux Mint 17.2 Cinnamon 64-bit, with Linux 3.16.0-38-generic' --class ubuntu --class gnu-linux --class gnu --class os $menuentry_id_option 'gnulinux-3.16.0-38-generic-advanced-b63f2ac6-42d2-48af-beeb-fb001b7c16b2' {
  recordfail
 savedefault
  load_video
  gfxmode $linux_gfx_mode
  insmod gzio
  insmod part_msdos
  insmod ext2
  set root='hd0,msdos2'
  if [ x$feature_platform_search_hint = xy ]; then
    search --no-floppy --fs-uuid --set=root --hint-bios=hd0,msdos2 --hint-efi=hd0,msdos2 --hint-baremetal=ahci0,msdos2 b63f2ac6-42d2-48af-beeb-fb001b7c16b2
  else
    search --no-floppy --fs-uuid --set=root b63f2ac6-42d2-48af-beeb-fb001b7c16b2
  fi
  echo 'Loading Linux 3.16.0-38-generic ...'
  linux /boot/vmlinuz-3.16.0-38-generic root=UUID=b63f2ac6-42d2-48af-beeb-fb001b7c16b2 ro persistent profile
  echo 'Loading initial ramdisk ...'
  initrd /boot/initrd.img-3.16.0-38-generic
 }
 menuentry 'Linux Mint 17.2 Cinnamon 64-bit, with Linux 3.16.0-38-generic (recovery mode)' --class ubuntu --class gnu-linux --class gnu --class os $menuentry_id_option 'gnulinux-3.16.0-38-generic-recovery-b63f2ac6-42d2-48af-beeb-fb001b7c16b2' {
  recordfail
  load_video
  insmod gzio
  insmod part_msdos
  insmod ext2
  set root='hd0,msdos2'
  if [ x$feature_platform_search_hint = xy ]; then
    search --no-floppy --fs-uuid --set=root --hint-bios=hd0,msdos2 --hint-efi=hd0,msdos2 --hint-baremetal=ahci0,msdos2 b63f2ac6-42d2-48af-beeb-fb001b7c16b2
  else
    search --no-floppy --fs-uuid --set=root b63f2ac6-42d2-48af-beeb-fb001b7c16b2
  fi
  echo 'Loading Linux 3.16.0-38-generic ...'
  linux /boot/vmlinuz-3.16.0-38-generic root=UUID=b63f2ac6-42d2-48af-beeb-fb001b7c16b2 ro recovery nomodeset persistent
  echo 'Loading initial ramdisk ...'
  initrd /boot/initrd.img-3.16.0-38-generic
 }
}

### END /etc/grub.d/10_linux ###

### BEGIN /etc/grub.d/10_lupin ###
### END /etc/grub.d/10_lupin ###

### BEGIN /etc/grub.d/20_linux_xen ###

### END /etc/grub.d/20_linux_xen ###

### BEGIN /etc/grub.d/20_memtest86+ ###
menuentry 'Memory test (memtest86+)' {
 insmod part_msdos
 insmod ext2
 set root='hd0,msdos2'
 if [ x$feature_platform_search_hint = xy ]; then
   search --no-floppy --fs-uuid --set=root --hint-bios=hd0,msdos2 --hint-efi=hd0,msdos2 --hint-baremetal=ahci0,msdos2 b63f2ac6-42d2-48af-beeb-fb001b7c16b2
 else
   search --no-floppy --fs-uuid --set=root b63f2ac6-42d2-48af-beeb-fb001b7c16b2
 fi
 knetbsd /boot/memtest86+.elf
}
menuentry 'Memory test (memtest86+, serial console 115200)' {
 insmod part_msdos
 insmod ext2
 set root='hd0,msdos2'
 if [ x$feature_platform_search_hint = xy ]; then
   search --no-floppy --fs-uuid --set=root --hint-bios=hd0,msdos2 --hint-efi=hd0,msdos2 --hint-baremetal=ahci0,msdos2 b63f2ac6-42d2-48af-beeb-fb001b7c16b2
 else
   search --no-floppy --fs-uuid --set=root b63f2ac6-42d2-48af-beeb-fb001b7c16b2
 fi
 linux16 /boot/memtest86+.bin console=ttyS0,115200n8
}
### END /etc/grub.d/20_memtest86+ ###

### BEGIN /etc/grub.d/30_os-prober ###
### END /etc/grub.d/30_os-prober ###

### BEGIN /etc/grub.d/30_uefi-firmware ###
### END /etc/grub.d/30_uefi-firmware ###

### BEGIN /etc/grub.d/40_custom ###
# This file provides an easy way to add custom menu entries. Simply type the
# menu entries you want to add after this comment. Be careful not to change
# the 'exec tail' line above.
### END /etc/grub.d/40_custom ###

### BEGIN /etc/grub.d/41_custom ###
if [ -f ${config_directory}/custom.cfg ]; then
  source ${config_directory}/custom.cfg
elif [ -z "${config_directory}" -a -f $prefix/custom.cfg ]; then
  source $prefix/custom.cfg;
fi
### END /etc/grub.d/41_custom ###

Is it possible to access your windows partition from linux? (file manager…)

Excellent question! Something sure doesn't look good but I'm not sure how to interpret it. Perhaps running the Grub Customizer was just a coincidence?!? In any case... thoughts?
Thanks for the great help so far!

I get this when I click on the volume :

Error mounting /dev/sda1 at /media/us/FC6ED1216ED0D60C: Command-line `mount -t "ntfs" -o "uhelper=udisks2,nodev,nosuid,uid=1000,gid=1000,dmask=0077,fmask=0177" "/dev/sda1" "/media/us/FC6ED1216ED0D60C"' exited with non-zero exit status 14: Windows is hibernated, refused to mount.
Failed to mount '/dev/sda1': Operation not permitted
The NTFS partition is in an unsafe state. Please resume and shutdown
Windows fully (no hibernation or fast restarting), or mount the volume
read-only with the 'ro' mount option.

And I looked up the 'df' command and ran that in the terminal and got this:

df: ‘/run/user/1000/gvfs’: Transport endpoint is not connected
Filesystem 1K-blocks Used Available Use% Mounted on
udev 4014476 4 4014472 1% /dev
tmpfs 806012 1560 804452 1% /run
/dev/sda2 31909772 8292964 21972828 28% /
none 4 0 4 0% /sys/fs/cgroup
none 5120 0 5120 0% /run/lock
none 4030048 46284 3983764 2% /run/shm
none 102400 16 102384 1% /run/user

The message says that your windows is hibernated. This may by the "fast boot".

Problem is: To resume your windows you have to boot it, but you cannot boot it cause grub didn't find it ;-)

So the only way is: adding a custom menuentry.
So add a new menuentry (there's a functionality inside of grub customizer) of type "chainloader" pointing to your windows partition. Then save and reboot. You should be able to boot your windows by selecting this menuentry.

Yes. Bit of a catch22. I'll give the fix a shot when I get home. Do you think this occurred because windows was in hibernation and then improperly shut down? Is it possible that this could happen again? Is there a way I can avoid it?
Thanks again for the great assistance!

It is just the hibernation. When windows is hibernated it's not a good idea to change files. However os-prober seems to mount the file system with read access.

You should disable fastboot or alternatively stick with your custom menuentry.