That's a known bug on the Mac. At some point during the window resize, the game thinks it has lost focus. It minimizes in response. Restoring it from its minimized state can result in it being stuck behind the "shielding window" created by the Mac OS X display capture function. It is also possible for display capture to freeze it part way through the "genie" effect.
At this point, the best you can do is a bit of dance with the Restore Display feature of CrossOver. Type Command-Option-R to force CrossOver out of full-screen mode. The game window should then be accessible, and you can quit it. Then, on the next start your video settings will be used right from the start and avoid this whole hassle.
Another approach is to use the launch options to pass "-width <w> -height <h>" to the game (where <w> and <h> are your desired width and height in pixels). Again, having the game start up in your desired resolution avoids the problem.
Sorry for the inconvenience.