Is it possible to prevent the window forms (Cell View, Object View, Render Window, Preview Window) from changing location?
It happens whenever I minimize CK and start Skyrim to check for bugs in my mods.

I'ts very annoying because I have to keep moving them back every time I come back from Skyrim.

Game running at the correct resolution for your monitor? Thats the only reason I can think, don't suffer from the problem myself.

My desktop resolution is 1280x1024, and Skyrim runs at 800x600. (Because I have a weak graphics card)

Could this be the reason?