I enabled FileVault, now my desktop background reverts to stock at each reboot?
This almost always has to do with corruption in the ~/Library since I've seen this come and go well before FileVault 2 came out.

Have you tried making a second user account and testing if the problem persists for a new user account?

If not, you'll need to poke into the ~/Library/Preferences folder, sort by date and see which files get updated when you change the desktop background and drag those preference files to the trash. (don't erase trash just yet in case you drag too many or the wrong preferences to trash).

Reboot and test - still not deleting the files. Once you think you've isolated the files (or file) where desktop pictures is stored, make a note of the file and empty the trash and the time.

That way if something else messes up, you can restore that file or resume the process of clearing selective preference files.