Hmmm changing the CPU might have done some kind of hardware refresh to your devices and that might have solved the problem. I was going to say you could also go to your BIOS and try to force an ESCD. If that didn't work, you could try loading the setup defaults in BIOS and work your way from there. You changed the card and re-loaded the OS but the BIOS settings had remained the same right? When you changed the CPU though, BIOS must have detected the new CPU and maybe forced the setup defaults as a result fixing something?
I also discovered something with the Catalyst drivers a while back. When you go to display settings by right clicking on the desktop and choosing display properties, under the advanced menus you might see that AGP might look like it is turned off. If you check with WCPUID though, it will say it is turned on and running at 4X. Then, if you go to the display properties through the ATI icon you can put on the taskbar by right clicking on that and THERE, even though that should take you to the exact same place, the AGP will show up as enabled and at 4x. Strange, no? Using the ATI icon or right clicking on the desktop and going to display properties should take you to the same place and it looks like it does altough doing it one way will tell you something else.
NOW, the PROBLEM here is if you try to set AGP to 4x when you saw it disabled under the display properties, then it will actually get disabled on the reboot! (and when this happens, you do see stuttering and even scrolling slowness of course like you said). By the way, this is done through the SmartGart tab under display properties. Also, if the second display under display properties got enabled by accident (you don't need to have a 2nd monitor attached physically to have it enabled) then there will be hella stuttering.
It looks like you solved your problem though but these are my ideas on what might have happened or might potentially happen in the future.