I'm having this same problem.
I currently have my ATI Radeon 8500 128 meg AGP on my left monitor (Primary, shows during boot)
and my ATI Radeon 7500 64meg PCI on my right monitor. (Secondary, standby mode during boot)
The "Primary AGP Card" window in the overclocking secion is greyed out while displayed on my AGP Primary monitor, but shows values from my PCI card (secondary, right monitor) When making change to the core/mem section my PCI (Secondary) is effected.
I've tried changing the driver install order with omega drivers , etc and re-installing ATITool but could not, for the life of me, get the values to show my AGP card. Finally I just disabled my PCI card and rebooted.. Once I launched ATI tool and clicked to see the 3D test, ATITool locked up and was shoing Core/Mem values of .1 (I'm assuming since the program seemed to be locked to the 64 meg card which was no longer enabled.)
I'm not trying to mooch on Viper's thread, I just wanted to confirm his error and possibly shed extra light on it.
Thanks in advance.