If you are using window capture and you don't want windows and such to appear on top, then you must enable aero. However, aero is bad if you use monitor capture at all. So you really need to choose between using window capture or using monitor capture, and have aero on if using window capture, and aero off if using monitor capture.
We can't know more without a log file at this point though, but I'm guessing that's your issue.