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.