I think what you're describing happens to me on occasion in CS 6 on Windows 7. I'm pretty sure it's only ever happened while RAM previewing with Render Multiple Frames Simultaneously enabled in a pretty heavy comp. If I click into another application and then click back to AE (dual monitors) it stops.
I always assumed it had something to do with the background processes momentarily tweaking out and sharing their bounteous wealth of crazy with the foreground app. I'll try to pay more attention next time it happens.
-Darby