well Sago knows linux a lot better than I do, and he knows the OpenArena code really really well....
The code is really split into 4 Major Segments....
Client Game Logic aka (cgame)
Server Game Logic aka (qagame)
User Interface Game Logic aka (ui)
cgame, qagame, and ui, they all run in their own virtual machine inside the engine...you won't have to worry about touching those
The engine code is split into various areas of interest...
If I am not mistaken, the 0.8.1 source for the engine really has more to do with the ioquake3 project than the OpenArena project...http://ioquake3.org
From the looks of it, the trouble is with the input/control part of the engine which pulls a ton from the SDL libraries...
I know it's not much...but sometimes stuff can go days without being answered