I think I know what is happening; though it is incredibly annoying. It seems that some condition causes an 'invisible' window to pop up which is taking all the input. The part that is super duper painful is that you can't see this window to remove it; and the program catches alt-del and alt-f4 but then this window auto-raises so you can't exit the game other than to log out (using alt-del).
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I found one of the invisible windows by hitting the chat button in the lower left corner; but I have no clue why it was popping up - there was no message (I was playing single player with the steam version) - but when i hit that button and then close the visible chat window the game became play-able again. Whatever is happening it is annoying as hell. It doesnt' seem to happen often - it happened once when I first started and now again 2 weeks later - funky little game.