Right clicking on a file of the same type and changing the default application via the properties does not help because GNOME default applications and system default applications are stored in two different lists.
To change the system default application (This will change the default application in Firefox):
1) sudo gedit /usr/share/applications/defaults.list
2) search and modify the line for appropriate file extension
To change the default application for GNOME:
1.a) sudo gedit /etc/gnome/defaults.list
2) search and modify the line for appropriate file extension
or
1.b) right click on file -> properties -> open with tab
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