I've never un-checked the "run in a window" selection as I don't want to run the game full screen, but I will see if that affects the resolution selection when I get home.
When "run in a window" is checked, there are definitely no resolutions in the combo box, and clicking "Play Game" just shuts down the launcher.
For now, here's my xrandr output: http://pastebin.com/jkVPNntK
In case it's relevant, the "primary" monitor is my small, "desktop things go here" monitor and is old and nvidia detects it incorrectly. Its max and native resolution is 1280x1024, and it operates there when gdm isn't running the show (but I'm not home to log in and make it switch).