Only full screen windows? Hmm that is a bit weird. I've never seen a virus or malware do this, but it can't hurt to scan for them.
Scan for viruses using your virus scanner, if it isn't up to date with the latest virus definitions, then go to
Housecall on Trend Micro's site for a free online virus scan.
I am wondering though if somehow a setting got changed in your display settings. On my crappy ol' computer I can't run Unreal with a full screen because I don't have a decent graphics card. Perhaps your settings got changed to a lower screen resolution and the program's or games you are trying need better graphics display.
Let me know if either one of these helps you out or gives a different result.