Since I found this with Google and I have a very similar problem, here is what I've found out: In my case the programme SynTPEnh.exe from the touchpad driver caused it. Sometimes, after minimizing a fullscreen window, this programme puts an invisible window in front of everything. Only ALT+TAB+MouseClick seems to work. Simple quick-fix: Kill the process and restart it (not a real fix but much of a relief for me). A simple batch file + Launchy makes this quite bearable.
taskkill /f /IM SynTPEnh.exe
start "" "C:\Program Files\Synaptics\SynTP\SynTPEnh.exe"