I guess I'll give up the game regardless if no one has a workaround. I would really prefer not to give up this game if at all possible, but there doesn't seem to be a way to access save via keyboard? If there is please let me know and I'll restart to see if it happens again.
I don't think it's an OS issue, as soon as I click back into FTL (or CMD-Tab) the pointer is again stuck. If I move out past the game window, the standard system pointer reappears and I can use it fine. I can move it left and right, but not down. When I opened laptop later to resume the mouse pointer is 'stuck' along the top edge of the game window. I had a game in progress earlier today, closed the laptop. Playing via Trackpad, no external mouse handy to test. MacBook Pro Retina, 15-inch, Late 2013 Up to date Mac OS
I'll post this via getsatisfaction as well, just putting it here in case anyone knows a quick fix.