This is true! Up until today my Preferences used to work fine in OS X, you could even select your theme from them. This was working from the first time I installed ST2. Now they are greyed out. I suspect it might have something to do with Ruby (please correct me here). I had to fight with it, reinstall it and Rails and gems in order to be able to use the gems mysql2 package with MAMP.
This is the only change I've made to my Mac and now the prefs don't work, however I cannot be sure it was this because I didn't check the prefs for a few days.
Is anyone else seeing the same thing?