Here are a few tips :
Rather than rebooting, switch to a console CTRL+ALT+F1 (or F2...), then log in, then :
Then kill openarena process
Or, rather than rebooting with CTRL+ALT+del, only shut down your X server, using CTRL+ALT+
Backspace.
For your problem with window minimized, so that it doesn't happen anymore, disable compiz before running OA ... and maybe disable your screensaver too (!)
IIRC,
(check other forum threads for other informations).
If it goes windowed, maybe you can take control of it again if you make appear the "in-game console", with Shift+Esc key. This helps in bringing back mouse+keyboard working with your desktop environment.