I confirm the problem.  Not sure if mine was also induced by .gvfs but
the effects are the same.  Baobab tells me my ~ folder uses 40G when the
real number is three times that.

** Changed in: gnome-utils (Ubuntu)
   Importance: Undecided => Medium

** Changed in: gnome-utils (Ubuntu)
       Status: New => Confirmed

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https://bugs.launchpad.net/bugs/822792

Title:
  Disk Usage Analyzer produce incorrect numbers on home directories

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