Fs2 open on Linux/Graphics Settings
From FreeSpace Wiki
|« Post-Compile Configuration||The fs2_open on Linux Guide|
|StartUp Script »|
Odds are, you'll want to run fs2_open in a higher resolution than the default 640x480. Since wxLauncher runs on Linux, use it to set your resolution.
Also, if you have problem running fullscreen with a dual-head config try setting this in the terminal you use to launch FSO: