I've not had this problem, but I've heard from somewhere (hell if I remember where) that high com_hunkmegs settings can do some silly stuff. Try setting it lower and see what happens --I run 192 and have never had a problem with it. It's also noted in the manual that anything higher than 128 or so really isn't necessary.
I don't think it could be that. I tried it by opening up the map with com_hunkmegs set to 300, and it worked fine. However, I usually run it at 256, and when I try entering a server for the first time I load GenArena it says "No or Bad Challenge for Address," but reconnecting fixes that. It never did that when I was on my stepdad's iMac (Where it was set to 192), so maybe my small problem's due to my com_hunkmegs being a bit high? Ah, well.