To change the default filemanager you can edit the file
~/.local/share/applications/mimeapps.list
Don't know how to specify thunar but to use nemo over nautilus I do this:
thomas@localhost ~> cat .local/share/applications/mimeapps.list [Added Associations] inode/directory=nemo.desktop;
Also if you are curious why the wrong filemanager is started if you click on a folder icon check the actual command the starter launches.
After resolving the issues (see comments) you also have to look in the file :
/usr/share/applications/mimeinfo.cache
there you can change the filemanager also:
inode/directory=nautilus.desktop inode/directory=nemo.desktop*