I got bitten by this bug tonight.  Like Dave Gross, I discovered that my
.Private directory had a bunch of empty directories with unencrypted
names in it -- corresponding to the directory names that were duplicated
(and empty) when my eCryptfs directory was mounted.  I fixed the problem
by renaming my .Private directory (with the encrypted directory
unmounted, of course!), creating a new .Private directory (with
identical ownership and permissions), and moving all (and only) the
ECRYPTFS* files/directories from my old .Private directory to the new
directory.  After doing this and remounting my encrypted directory,
everything was fine.  How the problem happened in the first place, I
have no idea.

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https://bugs.launchpad.net/bugs/623708

Title:
  duplicate files/directories when mounted

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