If you have tried to disable the onboard in the BIOS, and have tried disabling it in Device Manager, and have tried removing its drivers, then you've pretty much covered the bases.
Were I sitting in front of it, I might be able to get it working, but that's still no promise it would work. You might have to take it in to a computer shop and let someone tinker with it.
While a dead AGP slot is a possibility, ATI's cards are also known to be finicky creatures.