On 3 occasions so far (out of ~20) since installing the new version I have had no mouse support when starting the game (cursor is visible, but does not respond at all).
Still trying to figure out what circumstances were the same that differed in other times, but it appears fairly random at the moment. One thing I have noted is that once I used Alt-Tab to try to swap back to another application and it had immediately highlighted the 3rd one along, not the second as expected. This seemed to indicate that possibly the second application (explorer in this case) had focus instead of pontifex. I haven't seen it since to verify one way or the other :/
Were you surfing while you were playing? If a page finishes loading when you are looking at another window, often explorer will try to steal focus. Since pontifex was running full screen (guessing) it might have stolen focus without minimizing the window. Has this still happened when you are no using explorer?
Yeah, I know what you mean, and yes, I was surfing at the time, but the explorer that I picked up on was just normal explorer, not internet explorer (explorer opened at the pontifex directory to be exact)