I never had legacy FileVault eat my homedir, but I did have issues with it forgetting what program was supposed to be used to open what kinds of files. Very strange, that.
From memory this was due to LaunchServices not waiting until the home directory was completely mounted, and thus launching with default prefs.
There was a workaround I had running for a while in a large deployment in the form of a logouthook that would copy the relevant prefs to a location that LaunchServices would find it before FileVault finished mounting the home directory.
There were a lot of corporate/education deployments running "legacy" FileVault who hadn't invested in PGP WDE or other commercial options, and I bet they haven't all upgraded instantly to the new FileVault when they moved to Lion.
