I had the EXACT same problem. They popped up whenever they felt like it, wheather you were playing a game or not, right over whatever you were doing, I was playing Counter Strike one time and one popped up and crashed my computer. I found this handy site that the folks at the university of Virginia have put up, it explains the problem, and tells you exactly how to fix it.
http://www.itc.virginia.edu/desktop/docs/messagepopup/
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