I know this is an old thread, but I recently had the same issue... I was missing at least 10GB of space, but couldn't get FileVault to give me it's usual "reclaim space?" option at shutdown/reboot (despite countless tries over 48 hrs).
This is the procedure to which I had to resort to forcibly reclaim missing free space on my FileVault-encrypted PowerBook G4...
I figured out how to force a space reclaim... but the process isn't exactly point-and-click.
•I mounted the PowerBook via Firewire target disk mode on my desktop G5 and copied over my PB account's .sparseimage file to my desktop (didn't want to work on the original file in case I screwed it up).
•Used the terminal command "hdiutil compact" on the .sparseimage file (type "hdiutil compact " (with a trailing space) then before hitting return, drag the icon of the .sparseimage file on to the terminal. That'll insert the path of the file. Hit return.)
•Let it run. Took about 15 minutes or so. On a 27GB .sparseimage, the procedure recovered 12.5GB!
•Deleted the original .sparseimage from my PowerBook, emptied the trash, and copied over the newly compacted one. Rebooted the PB, and voila!