I attempted to install it with the zip file only.
It was a graphical distortion problem, but it's a ID/Steam problem, not a Generation Arena problem.
I apologize for blaming the bug on GenArena, but after more debugging and research I discovered what the issue was. The problem is purely graphical and it appears ID has no intention of ever fixing it. It seems like it wouldn't be worth the energy to port GenArena over to Steam.
For more information, I linked the thread in Steam support here:
http://forums.steampowered.com/forums/showthread.php?t=723156.
I'll catch you fine folks later.