I had to ignore my unwritten rule about never ever installing MacOSX as an "Upgrade Install". I have always used either "Erase and Install" or "Archive and Install" to avoid issues wrt versions, overwriting etc...
When I upgraded the OS on commons.ucalgary.ca, I didn't have a spare drive to use (well, I have the drive, and it's sitting in the server - it just isn't hooked up) so I did an upgrade. Big. Mistake.
Most of the stuff works fine, but I just tried upgrading the installed MovableType to use MySQL rather than BerkeleyDB (which has a corrupt record in it, and I'm very nervous about databases that don't let you run checks and fixes - I could fix the problem easily in MySQL).
Except that the required Perl modules aren't there (they should be). And, they won't install, since some of the old Perl 5.6 stuff is still in place, and seems to be confusing things. I'm going to try installing the dev. tools (as recommended on some of the lists), but there isn't a whole heckovalotta space left on that drive (less than 6GB, which makes me a bit nervous, too...)
Anyway, here's the MacOSX Mantra du jour: Never Upgrade. Always clean install (archive and install, or erase and install).