This has happened to me recently. I have logged in and all my GNOME
preferences went missing, and my home directory contained a lot of
directories similar to the ones in comment #13. After re-logging in
(maybe a few times, I might have not checked my home dir), my GNOME
settings were still missing, but my directories and files are back. It
seems to me as if after one login my home directory wasn't mounted
properly and GNOME has recreated the settings and default directories,
as they seemed to be missing, and when it's finally mounted them
properly, it uses the ones it's created, since it now has duplicate
directories (maybe it's overwritten the old ones, I can't tell because
regardless which of the duplicate directories I enter, I end up in the
same directory).

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

Title:
  duplicate files/directories when mounted

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