So it turns out the bug I was seeing was a manifestation of this bug:
Updating to xorg-x11-server-Xorg-18.104.22.168 fixed the problem for the better part. However I still do get occasional graphical artifacts in the form of squares that follow the cursor but only on one particular monitor, the middle 30" monitor. All other monitors are fine, and obviously this was not the case with fedora 11 so I know the hardware is good. Anyone has any ideas?