After installing xubuntu packages in order to check xfce, I reverted back to gnome2.
During the first login, I noticed that thunar was now selected as the default file manager.

Preferred applications menu is also missing now, so I could not set nautilus as the default. I removed all the xubuntu packages (including thunar) and then when I tried to open a folder, I was asked to select the default file manager - that's how I got nautilus back.

The next problem I'm now facing has to do with the downloaded files from web browsers:

Open and Open containing folder options produce exactly the same result.
If I double-click on a file, it'll just open the containing folder, instead of opening the file with it's associated application (e.g. libreoffice writer for .doc,.odt, smplayer for .avi,.wmv, etc).

The problem happens both in Firefox and Chrome.

Through nautilus, all files open correctly.

Up until now I've tried the following:

• Delete/recreate mimeTypes.rdf in my FF profile
• Create a new profile in FF
• Delete/recreate ~/.local/share/applications/mimeapps.list
• Already checked this similar article

None of them worked.

Any ideas on the issue would be appreciated.