I ran into a problem the other day on both 8.1 and 9 for the Mac: while drafting the shift keys wouldn't constrain the mouse to the preset, or custom set, angle constraints. I also could not get the eyedropper to activate to match attributes. Basically no keyboard modifier keys worked.
After lots of time going back and forth with tech support over several days, I noticed the same problem in Adobe Illustrator CS and found the solution in their forums.
It ended up being the autoupdate deamon for Quicken (a little invisible system process that schedules updates to the quicken file from external data sources).
Bizarre, but at least it's now part of the collective consciousness.