I have the same gvfs* packages with same versions.

Although, I remember doing one thing before ... I removed metadata information 
about Desktop from ~/.nautilus/metafiles. I did this:
cd ~/.nautilus/metafiles
find | grep Desktop.xml
...and removed that file and restarted nautilus (relogin or killall nautilus)

But I'm not sure this is the solution.

-- 
desktop icon position of symbolic links are not restored 
https://bugs.launchpad.net/bugs/411322
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