SDL (which we use) has some problems when running fullscreen on non-native resolutions (that is: different from your desktop resolution), you can try two things:
1) You can use a custom resolution to match your desktop's: Start the game with the following parameters:
+set vid_mode -1 +set vid_width 1600 +set vid_height 900 (you can also
find the configuration file and edit the values there)
2) If you want to use a different resolution you can try to use the "true fullscreen" mode: While running the game Hit
[ALT]+[ENTER] to go to windowed mode, then hit
[CTRL]+[ENTER] to go to "true fullscreen"
Or, of course, you can try to play in windowed mode (you might want to enable mouse grabbing with
[CTRL]+[G] if you do)