If you happen to have a nVidia graphics card and the 77.72 drivers, it is very well possible that this is a nVidia thing.
I had the very same problem (and a couple of others) after updating to 77.72 drivers.
The Desktop Manager would suddenly swap display 1 and display 2, assign random sizes (and I mean random) to explorer or browser windows, sometimes open them maximized, and show all dialog boxes on the secondary display.
Luckily, the dialog box thing can be configured under Desktop Management -> Windows -> Move Dialog boxes to display...
I had to toggle it forth and back a few times, but eventually it worked.