Heh!
I made the mistake of preording rebellion and this multi-monitor bug was never addressed. In fact, one of the devs (Yarlen maybe?) had the audacity to say that they "couldnt replicate the problem".
It's been here since rebellion.
I have 3 monitors and this is a game breaker for me.
Now they want more money for dlc? ugh. what a joke.
Sorry for the rant. I'm so disappointed in Star Dock...
Likely someone will come along and mention an external program that keeps your mouse locked in.
I vaguely recall a workaround....something like setting your resolution to something else, then NOT clicking "accept" the changes.
Hope that helps