I don't know if this one has been mentioned yet. Whenever I save a prototype for a particular object, Max deletes all the previous prototypes and replaces them with the just saved prototype. Luckily, I back up my patches about once a week...because I just lost all of my b-patcher prototypes! I know it's a beta, so no hard feelings!
Also, I made a post a while back that freqshift~ doesn't function at all in the current release. It seems to attenuate the signal a bit, though. I get this problem even from the help file. I didn't get a response, which is no big deal (I'm sure you guys are busy). I just didn't want it to get overlooked.
Mac OSX 10.4.7
1.83 GHz Intel Core Duo
1.5 GB DDR2 SDRAM