It actually appears to be less predictable than I thought in my last post.
Today I loaded up a project (2 instances of Metaplugin, one with 2 Nebulas and one with 4 Nebulas). Started Pro Tools from scratch, loaded the session, all 6 instances came up <- 44100 blinking arrow
Out of curiosity (based on behavior I saw yesterday afternoon) I reloaded each instance, saved the session and closed it. Relaunched the session (without quitting Pro Tools). All 6 instances came up loaded correctly.
Not sure what exactly the pattern is; we'll be keeping an eye on it obviously but I don't have any more time today for dedicated testing, maybe tomorrow. Weird, though.
All of this, incidentally, is on .492 (after .602 I'm waiting until I see a whole bunch of successful reports for a 32-bit OS X client before I even think about updating).