There are many segments in BG&E that require you to remain crouched for long periods of time. Occasionally during these segments, after having been crouched for more than 10 seconds or so, it will pop me out of the game to the windows desktop, and open a Windows Explorer window to Start Menu\Programs. Once I click back into the game, every time I tap ctl to crouch, it will open another explorer window and bump me to the desktop.
Anyone had an issue like this, or have suggestions as how to prevent it?

Not sure if thats a windows setting but you may want to check to make sure your keyboard is clean it sounds like holding control is sticking down the windows button next to it. You could try changing the crouch button from the start menu you can find the Beyond Good and Evil settings and rebind the crouch key to something else. Try this and see if its still kicking you out to windows or not while crouching.

you should change your settings m8
if you go to start , settings , accessibility
there you turn of sticky keys. I have had this problem a lot while playing counterstrike.
When i crouch i got a desktopview after 5 seconds in the heat of the battle.
Turning this of solved the problem.