I put the same mobo in my daughter's computer when I upgraded it. You did load the AGP 2.0 driver utility from the disk, didn't you (just had to ask)? If this is the case, there could be a problem with the bios version. After I upgraded my daughter's and installed a 7600 GS with 512 megs onboard RAM, I had to update the board bios. That's not to say it is the problem here. It could be that once the drivers for the AGP interface is installed, the drivers are working, but the card may be bad. Remember, when reinstalling Windows, it will load a generic VGA driver for your card. The card really isn't being run through its paces until the AGP driver interface is installed.
Do you know someone where you can take out your card and test it in their rig? I would advise that prior to updating the bios. The thing about bios is, "If it ain't broke, don't fix it". That would be my first step at resolving the problem. Make sure you have the lates version of the graphics drivers (Forceware 163.44). They are beta and you'll get the "The driver you are trying to install has not passed the Microsoft WHQL certification..." but don't worry, I'm running them because they are the version required for Bioshock and I haven't had any problems with them.
Let me know what's up and where we need to go from that point.