I'm sorry it took so long to reply. We had a problem with the forums over the weekend, and we've been busy recovering from that.

Could you tell me a little bit more about this situation? Do you remember exactly how you paused and unpaused the game? Was the game left on, or did you quit (either from the Main Menu or using the "X" on the window) after you paused it? When you returned to the game, did it actually say "GAME PAUSED" at the bottom of the screen?

We are working on high-priority bugs, but we have never seen a game do what you described. Unless we can recreate it, we have only a slim possibility of figuring out what's happening, which is required in order to fix it.