Overall 10.3.9 sounds promising but imperfect. I'll wait another week.
Update: Sounds like it's caused by having java running somewhere (other user space) preventing the update. In theory this is allowed, but in practice here's the superstition I follow for major OS X updates (XP updates, in my experience, have not required this sort of superstition):
1. log in on my very plain admin account (no odd configuration, no startup items, etc). Run PCC (or similar) to flush caches.I sometimes "repair privileges after #4, but I think that's less important.
2. shut down, restart and login again to admin
3. run the update
4. shut down and restart