When in Centos 7.1 I clicked on a *.doc file created by LibreOffice, gedit was run, even though the icon and the mime type (reported by “xdg-mime query filetype”) were right. Other users didn’t have that problem. I fixed this by removing ~/.local but not before fruitlessly removing ~/.gconfd, ~/.gconf, ~/.gnome2, ~/.gnome, ~/.nautilus, ~/.config and ~/.cache. If users (especially people who’s been here for years) are having desktop problems, you might suggest to them that they try blowing away all these folders.
I’ve written about some of this in The Nautilus File Manager – internals