Still happening.  Skype seems to exacerbate the situation.

$ find $HOME/.Private/ -size 0c -exec ls '{}' \; | wc -l
find: 
`/home/xxx/.Private/ECRYPTFS_FNEK_ENCRYPTED.FWYQViTKpRilBEQrvyhYzFbx53yokrMo5MdfE-hi0ZqRBXpRjN1jF7OjKU--/ECRYPTFS_FNEK_ENCRYPTED.FXYQViTKpRilBEQrvyhYzFbx53yokrMo5Mdf6-WXCmCjMQFUqNo4qH2x0HeJB218Tn.XH.DMCOJ9MTQ-':
 Permission denied
3
$ uname -a
Linux paperweight 3.0.0-16-generic #28-Ubuntu SMP Fri Jan 27 17:44:39 UTC 2012 
x86_64 x86_64 x86_64 GNU/Linux
n

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https://bugs.launchpad.net/bugs/509180

Title:
  ecryptfs sometimes seems to add trailing garbage to encrypted files

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