Wollo:
the pausing, yes.
Actually, I am quite happy about FS minimizing when I go off screen with synergy, because it minimizes in 3 windows (and reopens them just like they were before). If I do an Alt Enter, I go back to all windows on top of each other and I have to undock them again...
Anyways, once my cockpit is up and running, there is no need for the mouse anymore. I try not to touch it, but to do all tasks during the flight by flipping switches, turning knobs etc. - that's why I spend all those 1000s of h building my cockpit, after all :-)
Regards,
Hans