Two video cards on same pc, problems with default GUI after upgrade

If you press CTRL+ALT+T

What is the output of:

sudo lshw -C display; lsb_release -a; uname -a

Thanks

 Original:

  *-display
       description: VGA compatible controller
       product: RS880 [Radeon HD 4200]
       vendor: Advanced Micro Devices [AMD] nee ATI
       physical id: 5
       bus info: pci@0000:01:05.0
       version: 00
       width: 32 bits
       clock: 33MHz
       capabilities: pm msi vga_controller bus_master cap_list rom
       configuration: driver=radeon latency=0
       resources: irq:18 memory:c0000000-cfffffff ioport:b000(size=256) memory:f9ff0000-f9ffffff memory:f9e00000-f9efffff
  *-display UNCLAIMED
       description: VGA compatible controller
       product: GT200b [GeForce GTX 275]
       vendor: NVIDIA Corporation
       physical id: 0
       bus info: pci@0000:02:00.0
       version: a1
       width: 64 bits
       clock: 33MHz
       capabilities: pm msi pciexpress vga_controller cap_list
       configuration: latency=0
       resources: memory:fd000000-fdffffff memory:d0000000-dfffffff memory:fa000000-fbffffff ioport:c800(size=128) memory:fe880000-fe8fffff
Distributor ID: Ubuntu
Description: Ubuntu 12.10
Release: 12.10
Codename: quantal
Linux mhhall-work 3.5.0-17-generic #28-Ubuntu SMP Tue Oct 9 19:31:23 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux

Stderr seems to have message:
No LSB modules are available.

Sounds like you may need to form an xorg.conf detailing both displays. This is the only way I have seen 2 differnent cards work well in Linux. Fareasier to buy 2 Nvidia or 2 AMD cards and have an easy life.

I'm really just trying to use the 2nd graphics card (nvidia) as a processor (no monitor connected).
I guess that I could reload (with the on-board GPU disabled), but I've been having issues getting
a nvidia driver to work (seems that 12.10 version won't let me use Jockey to install the 3rd party
nvidia drivers).

Looked like I had things working prior to last software update.

Seems like there ought to be some way to reset my GUI (remove / change something in my account) so that the GUI settings are reset.

Just disable the onboard in BIOS, no need to reinstall. Should be ok

When running with the nvidia card as primary, I'm still seeing same GUI problem (can't see the "dash" items to launch applications).

I also am unable to run BOINC / GPU application (which appears to need some version of nvidia driver installed).

Run:

sudo apt-get install nvidia-current

Reboot to test. You can do this in the terminal with:

sudo reboot

:)