Based on the Linux executables a few users were kind enough to port my game to, fullscreen appears to be broken. Both with global game settings and window_set_fullscreen(1). Instead of running in fullscreen, the window is just maximised, therefore still in windowed mode.
window_set_fullscreen(true);in an object works for me, however setting "Start in fullscreen mode" starts the game and moves it to the top left corner of the screen.
What desktop environment are you using? Full-screen isn't some special mode; you just remove the window's frame and maximize it. If your Window Manager is ignoring my instructions to remove the window decorations, that sounds like a bug on its end.
The failure to start fullscreen sounds like a legitimate bug, though. Kind of amusing.