Strange behavior after software update

I'm working with a 13" MacBook running OS X 10.4.11. Recently, the owner ran Software Update to download the most recent security update. On shutting down before restarting, she was prompted to recover unused space in her Filevault-protected home directory. The recovery process hung, and she was forced to force-restart the Mac. And that's when things got weird ...
The Mac now exhibits all kinds of odd behavior, including widespread amnesia with regard to its preference files. Several applications - Mail, iChat, Address Book etc. - will randomly 'forget' all their stored data and revert to the 'never used before state'. iTunes repeatedly complains that its library file is corrupt. Mail attachments go missing. The Address Book lost all its data, and it took multiple attempts to get it to re-read the backed-up version of the data file. The Console indicates some errors reading plist files. Downloaded files appear damaged (trying to download the OS X 10.4.11 Combo Update, for instance, resulted in failed verification) although downloading them to another volume seems to work.
TechTool 3.11 doesn't indicate any problems with the computer, and following the Apple-recommended procedure for verifying a sparse image (i.e. a FileVault home directory) didn't report any errors. However, it's pretty clear that something is very wrong.
Has anyone seen this issue before, and found a fix? Or is the best solution to nuke and reinstall the OS from zero, then restore all the user's data from backups?

One other possibility would be to reapply that update and/or the The combo update for Intel-based Macs...
http://www.apple.com/support/downloads/macosx10411comboupdateintel.html
Repair Permissions before & after re-install, then reboot again each time.

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