Why can't I make a file association in Nautilus?
Solution 1:
I had the same issue with Nautilus not allowing me to set acroread as the default for pdf files. Perhaps you can use something like I did to fix things up. Like you, mimeopen worked fine.
xdg-mime query default application/pdf # show current association
xdg-mime default /usr/share/applications/acroread.desktop application/pdf
This also made firefox open my pdf links with acroread, which was my real goal, because the default evince "Document Viewer" doesn't open up tab panes and opening up 10+ separate viewers with the Unity desktop is r-e-a-l-l-y painful.
Maybe a similar use of xdg-mime can fix your setup too?
Solution 2:
A very simple solution: You can use PCManFM to add file associations, and these are then shown in Nautilus.