Yes I believe this IS normal. I get the same message every once in a while. I think if you do a lot in your home folder (including things on the desktop) then the filevault needs to reclaim/declaim that space. There was an issue where File Vault could potentially loose your data while doing this, but its been fixed in the OS X.3.1 update.
I hope Apple will figure out a way where I don't get this message. I usually get it when I go to shut down, or log out of my computer.