Since you have identified a specific file which seems to be read in two
different ways, it might be useful to capture the actual content of the
file in each case (not just the md5sum values) and see if there is any
discernible pattern to the corruption (e.g., extraneous trailing nulls
in one of the two versions).

And if the corruption happens only with files that have more than one
hard link, this might help explain why some people have not reported
seeing the problem.

I've upgraded all five Ubuntu systems under my control to the latest
Natty kernel (2.6.38-11.50), but I'm obviously still nervous as long as
this bug appears to be evident.

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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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