I also have 12.04 and see many errors like these:

Sep  7 21:53:01 CCCx kernel: [ 1031.641254] Either the lower file is not in a 
valid eCryptfs format, or the key could not be r
etrieved. Plaintext passthrough mode is not enabled; returning -EIO
Sep  7 21:53:01 CCCux kernel: [ 1031.641340] Valid eCryptfs headers not found 
in file header region or xattr region, inode 8395
690

then my pc reboots, and I see these during boot.

Sep  7 21:56:35 CCux kernel: [   10.858208] EXT4-fs (sdb1):
ext4_orphan_cleanup: deleting unreferenced inode 8388879

not sure if this is what crashes my system, but the messages are the
last things I see in my syslog each time I crash

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https://bugs.launchpad.net/bugs/911507

Title:
  eCryptfs should initialize existing empty files at open()

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