Stupid El Capitan :(

 From:  Michael Gibson
7783.17 In reply to 7783.16 
Hi Blade - it has to do with the multiple monitors. The "Wineskin" system that the MoI Mac version currently uses has not yet caught up to changes in how multiple monitors work in recent Mac OS versions.

There is a system setting that you can change to go back to the previous style OS multi-monitor behavior which should then make MoI work ok. That setting is under System Preferences > Mission Control - uncheck "Displays have separate Spaces" there. You will then need to reboot your system in order for this change to take effect.

This should be fixed up better in MoI v4 which will not use the wineskin mechanism anymore, but it will still be a while yet before v4 is ready.

- Michael