could be the primery display is still set to pci and your using agp,
or it could even be a corrupt bois, without seeing the bios myself i couldnt tell, as there are so many different settings that effect it.
one thing i would try tho, make a note of your current settings then reset the bios to default values. this will tell you if it was caused the the 'tinkering' factor.
if theres any setting your unsure of , go to
www.whatis.com and do a seach on it there to tell u what it is/ does, you could try the radiobot geekspeak dictionry, but its not finished yet so may not have to answers you need