I know this is a long shot, but assuming there isn't anything that can help with this annoyance (in say Tweak7, etc), perhaps someone at Stardock will think this sounds like a good feature to include somewhere.
I run screen savers and I tend to have a lot of windows up--some maximized, and some 'docked' to the left or right half of the monitor using the Windows 7 'drag to side' feature. After a screen saver exits, since they run at much lower resolutions, any windowed/maximized or even 'docked' windows get moved and resized smaller. Friggin annoying!!!
Does Stardock have anything that may help with this stupid annoyance?