Hi yophie, Apple made some significant changes in the way multiple monitors work in OSX Mavericks, and XQuartz which MoI currently uses still has not caught up to those changes.
I think it's scheduled to be fixed in a future version of XQuartz, but for now you should probably be able to solve the problem by changing the setting to return to previous style multimonitor behavior. 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.
Hopefully that will stabilize things for you.
- Michael
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