I also have encrypted home and had this problem. The workaround appears
to work for me. It was preventing me from openign files via sftp mounts
with Geany, and now that works ok.

I've been getting all sorts of random crashes on 12.04 so hard to say if
something else isn't wrong. It's been very unstable for me.

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https://bugs.launchpad.net/bugs/995543

Title:
  [precise] .gvfs fuse mount is not functional after logout and
  subsequent login

Status in eCryptfs:
  Confirmed
Status in “gvfs” package in Ubuntu:
  Confirmed

Bug description:
  Looks like bug 212789 is back, at least the symptoms are the same.

  When I log out, the .gvfs entry stays in /etc/mtab (checked by logging into a 
console as root).
  This seems to be a stale entry, though, as it is not listed in 
/proc/self/mounts.
  Still, when I log back in, any operation on .gvfs gives "Transport endpoint 
is not connected" (that means non-gnome apps cannot access remote files).

  After logout,
  # umount --fake (as root)
  gets rid of the entry. When logging in again with my user, .gvfs works.

  ProblemType: Bug
  DistroRelease: Ubuntu 12.04
  Package: gvfs 1.12.1-0ubuntu1
  ProcVersionSignature: Ubuntu 3.2.0-24.37-generic 3.2.14
  Uname: Linux 3.2.0-24-generic x86_64
  ApportVersion: 2.0.1-0ubuntu7
  Architecture: amd64
  Date: Sun May  6 18:36:55 2012
  EcryptfsInUse: Yes
  InstallationMedia: Ubuntu 12.04 LTS "Precise Pangolin" - Beta amd64 (20120328)
  SourcePackage: gvfs
  UpgradeStatus: No upgrade log present (probably fresh install)

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