In Diablo II, a friend would set alt for a commonly used button, such as highlight treasure or run, so they were holding that button down a lot.
When it was time to use a potion, they would be hasty and occasionally miss the "4" key and end up pressing "F4" instead.
Your tale of this happening once every 10 missions sounds like a similar time frame as that accidental Alt + F4 combo, with similar consequences.
Windows 7 added a few more minimize to desktop options, are you accidentally hitting one of those?
http://en.wikipedia.org/wiki/Table_of_keyboard_shortcuts
Hmm, not listed are some of the mouse things, such as grabbing a window and wiggling left and right a few times quickly.
(Is it possible that while you are holding down left click to shoot and then wiggle left and right to spray bullets back and forth that it is triggering that command?)
Personally, I used to find the Left Windows key to be rather devastating for similar reasons, so I have performed Hardware "enhancements" to remove it from my keyboard(s) in the past. There is still a Windows Key on the right if I ever needed to press it.
Some other things that may do it:
Do you have a mouse with additional features beyond left, right, and scroll?
Do you have any other software running in the background that likes to get attention periodically? (AVG and USB Wireless software are two examples.)
Do you have any special keyboard commands or Macros set-up?
Any accessibility options interfering?
Did you adjust the Key Binding to something different? (I did and it helps a lot)