Dual-booting Windows 7 and Ubuntu 12.04 LTS.

I went to reboot from Win to Ubu, and found a few interesting things.

My POST screen is covered in blocks of epileptic colors until I hit GRUB, which continues when I try to boot into Ubuntu. These color blocks don't appear when I use my on-board VGA, so I'll just attribute to that.

Grub dimensions are swapped (card vs onboard, probably), but, when interfacing with onboard VGA, the Grub Timeout Counter works and when using my card, it does not (see "[!!!]" below for more information)

Booting into Ubuntu directly causes the error:

SP5100 TCO timer: mmio address 0xfec000f0 already in use

Booting into recovery mode, meanwhile, and then "resuming normal boot" gets me to the desktop without native 1440x900 resolution and graphic drivers can't tell the monitor it's looking at (I assume this is because it's not a full graphic boot, and as it says, some drivers won't run?) [!!!] When I reboot after going into recovery mode, the countdown timer works ONCE, puts me back into default ubuntu boot, and then does not work again until after another recovery-mode boot.

Windows 7 can boot perfectly with no issues whatsoever from epilepsy color blocks or driver detection. This makes me wonder /why/ the POST screen can't handle my video card anymore.

Amidst all the diagnostics, I opened my case and re-seated the videocard securely, ensuring it wasn't a loose connection-- But this did nothing to help me.

Hardware
I am running an NVidia GeForce GTX 8800 video card in a PCI slot. I have 4.8GiB memory, an AMD Athlon II Quad-core 640 Processor, on an MSI K9N6GM Series Mobo. Onboard video is an NVidia GeForce MCP61(V/S/P) card.

Note: I did not have any of these problems yesterday, and I have been using Ubuntu intensively for a week, though it's been working flawlessly for months. I've recently been using it to mod my Android phone, perhaps I messed something up in the file system?