I don't quite know what could be happening but to make your favorite file
manager default, you have to use the xdg standards:
Look, to make your beloved pcmanfm the default manager, put this on the
terminal:
$ xdg-mime default pcmanfm.desktop inode/directory
If you change your idea and want another file manager, switch pcmanfm.desktop
for the file that corresponds to the file manager you want in
"/usr/share/applications".
the file that handles these defaults are located in
"~/.local/applications/mimeapps.list".
I hopped It worked.
