Apple posted a knowledgebase article that reveals that the Mac OS X 10.3.1 update does specifically address the FileVault preference corruption that could occur with Mac OS X 10.3.
- FileVault normally asks to reclaim space before the computer sleeps, restarts, or shuts down. In some cases, you can lose some preference settings after space is reclaimed. Download and install Mac OS X 10.3.1 or later to avoid this issue.
Note: the update does not restore any previously lost preferences.