I was hoping they would have added an update to the menus, they say in their changelog that they have (but no info on changes)http://icculus.org/alienarena/changelogs/7.30.txt
47. Updated menus with new options. http://ubuntuforums.org/showthread.php?t=1192175
--there is also a config file (code ?? can't find the name at the moment, it is in /home/.code* along with /home/.arena), that may offer some info for you..
I also, since I haven't played it for awhile, don't remember if there was a chkpoint option within that game
--if there was, perhaps it could be started from that save point ?