This is still an issue for Jaunty, but users can add the following to 
/etc/apparmor.d/abstractions/base to work around the problem:
  # encrypted ~/.Private and old-style encrypted $HOME
  owner @{HOME}/.Private/** mrixwlk,
  # new-style encrypted $HOME
  owner @{HOMEDIRS}/.ecryptfs/*/.Private/** mrixwlk,

You'll need to reload apparmor before this is in effect. Note that this
is a temporary workaround until upstream handles stacked filesystems
generally.

** Summary changed:

- apparmor paths are broken when using ecryptfs on jaunty
+ apparmor paths are broken when using ecryptfs

-- 
apparmor paths are broken when using ecryptfs
https://bugs.launchpad.net/bugs/359338
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