I've tried both the checkbox and without the checkbox for 'Run in Window' and neither seemed to place the game in a window.
I'm running 3 monitors with a max resolution of 5760x1080 and Xenonaughts doesn't scale well to that resolution, so I set the resolution to 1920x1080 which works great except that it blanks out the left and right monitors. I would like to set it up so that I can use my other screens for surfing, teamspeak and the manual etc.
Is there some way to set this up via the ini files manually?