Right, the issue is that .etckeeper permissions tracking is not
completely integrated into git (or bzr, for that matter).

You need to run "etckeeper pre-commit" to regenerate the .etckeeper
file, before running status :) If you ignore .etckeeper, then
permissions changes would not be committed.

If you are interested in better integration of .etckeeper into the VCS actions, 
please see:
Bug 322327       Integrated permissions/ownership diff output for etckeeper/bzr
Bug 322339       Integrated permissions/ownership reset on file operations for 
etckeeper/bzr

** Changed in: etckeeper (Ubuntu)
       Status: Incomplete => Invalid

-- 
.etckeeper file should be added to .gitignore
https://bugs.launchpad.net/bugs/618600
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