Odd system problem here. I'm running Vista on a laptop with an external monitor. However, every now and then (every few minutes) the external monitor goes black for a second or two, and sometimes some of the windows from there get moved over to the laptop's LCD. It's as if the monitor's been disconnected and reconnected.
Possibly useful: this thread suggests disabling TMM in the task scheduler. Looking this up, it's the Microsoft Transient Multi-Monitor Manager, which sounds relevant.