Just recently I had lots of weird things happening on my desktop. The Places-addon of Xfce4 was for example opening always my mp3-player qmmp, when I clicked on a folder. Interesting default?! Also when opening pdf and epub-files always calibre was the default.
Digging through the net, I found this:
http://ubuntuforums.org/archive/index.php/t-51012.html
So basically I removed the local apps associations (rm -R ~/.local/share/applications/*) and edited /usr/share/applications/defaults.list (there calibre installed itself). This actually did not help too much. I found a very interesting command: mimeopen
So concering fixing the folders, I tried mimeopen on the command line and it asked me which default folder-opener I wanted and I picked thunar, which fixed this problem.
So, use the tricks from the link + mimeopen.
When mimeopen opens the right stuff, your system should work.
Good luck, fixing!