I don't know if it's called preferences. It'll probably be more like config.something. I don't really game on a mac, and havent been too concerned even though this problem is annoying. My guess is that it is in application support under the game title. If I get around to checking this out i'll post ...

I haven't tried it, but forcing the window res in the game preferences might work.

I am having the exact same problem. Every time I adjust the windowed option to no, I get an error stating "failure to set screen" and I end up with a strange off centered window of the game running but not correctly displaying all contents.