It happened to me too and it seems like non-GTK apps can't see the font variants. E.g. in Firefox, where I used to have three subfamilies for DejaVu Sans (Condensed and two others that I can't remember : maybe Condensed Oblique and Condensed Bold), I now have :
DejaVu Sans
DejaVu Sans
DejaVu Sans
If I set DejaVu Sans Condensed in the fonts config of Gnome, the font appears correctly in GTK apps but not in others (menus of Firefox, openOffice...).
It happened to me too and it seems like non-GTK apps can't see the font variants. E.g. in Firefox, where I used to have three subfamilies for DejaVu Sans (Condensed and two others that I can't remember : maybe Condensed Oblique and Condensed Bold), I now have :
DejaVu Sans
DejaVu Sans
DejaVu Sans
If I set DejaVu Sans Condensed in the fonts config of Gnome, the font appears correctly in GTK apps but not in others (menus of Firefox, openOffice...).