I have this problem for two days now. First when it happened, logging out and back in helped, but now this occurs right after booting. I cannot activate any window by clicking into it, and also cannot minimalise, or close it with mouse. In few applications I cannot even interact with them with mouse (e.g. clicking on links in browser). I can scroll an active window with the trackball, and sometimes everything works normally for a little while. Everything works fine, when I use keyboard for this, I can resize, move, close windows with keyboard shortcuts, etc.
I ran a complete Avast! scan, but it found nothing important. Also event viewer did not show any relevant errors. Here's a log from HijackThis if it helps anything.