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.
My Rig: SABLE
Antec 300 Illusion / Antec EarthWatts EA650 650W / EVGA GTX 760 2GB
AMD FX 8320 x8 Black Edition / Gelid Tranquillo / MSI 970A-G43
Sandisk Ultra Plus 128GB / Samsung 840 120GB / WD Black 750GB / WD Green 1TB / WD Red 3TB
G.SKILL Ripjaws 2x2GB DDR3 1600 - Crucial Ballistix Tracer 2x2GB DDR3 1600
Win7 Ult 64-bit - Func MS3 Mouse - CM Storm QuickFire Rapid Mech Keyboard
R.I.P. Danny L. Trotter
... 14 Nov 1945 - 4 Sept 2009