Comment 16 for bug 63403

Well, it's not your fault, the fact that you've different way to configure fontconfig is quite odd, and I don't know how it can handled correctly, and I don't know why all apps don't react the same way.
The ~/.fonts.conf was most likely created by kde.
Gnome only exports Xft resources. Kde does that too, but also write the ~/.fonts.conf file.
So I don't even know if it's a gnome, kde, or fontconfig bug :p