I'm not an expert but it sounds like some program which may be running in the background is stealing focus, which can happen even without a new window appearing. I've read a few articles about Gmail's windows stealing focus all the time with Internet Explorer, and people have suggested changing browsers to Mozilla or Firefox, but that seems a bit drastic. Press Ctrl+Alt+Delete and see what is running, perhaps a lot of it can be terminated. If you do find anything that isn't necessary you should stop it from starting at bootup by using msconfig (click Start > Run > msconfig, then click the startup tab and uncheck anything you don't need). I think there are a few tweaks which can be applied to Windows in general which prevent windows from stealing focus. Maybe some sort of browser sheild like SpywareBlaster or ScriptDefender could help. The problem may not be spyware related but those programs have other little functions that deal with general browser settings as well as security.
I hope this is of some use! lol Good luck.