It seems this error happens when one attempts to use the ecryptfs utilities while logged in over an SSH session. Using a terminal right on the machine, things work as expected. If the SSH behavior is expected (should it be documented?) then this bug report could be closed.
- Bug#931208: ecryptfs-utils: Has ecryptfs lost sync with kernel? clayton
- Bug#931208: Acknowledgement (ecryptfs-utils: Has ecryptfs los... Clayton