Nothing happens after the active window minimizes (e.g. a tooltip balloon from the system tray)? Does this happen only with WoW, or any window? (Also non-fullscreen windows?)
I would check what programs/processes are running while this is happening (in task manager) and try to eliminate any one that may cause it. Also, I would look in event viewer to see if anything there might be correlated with the timing of the minimize. (Post screenshots if you want another pair of eyes to look over these)
I'm not sure what are the odds that this is related, but I would try running a bit without Aero and see if it still happens (if Aero is on while this is happening).