Not exactly helpful for the bug report, but a hint at Erik: I have found quite 
a few traps in Ubuntu Software where it is assumed that the root user has 
access to the user's home directory, which is not the case in such an 
environment. Examples include usb-creator (fixed by now), pam_mount and others. 
This is a side effect of the Ubuntu way of allowing "normal" users to do 
administrative tasks via sudo.
Applications using PolicyKit apparently do not suffer from this, obviously 
usb-creator is a good example for this.

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gvfs-fuse fails to start on NFS mounted homes
https://bugs.launchpad.net/bugs/435719
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