I'm glad I found this bug report. I just upgraded two machines from 12.04 to 12.10 and only one of them was giving the warning, even though they have identical 50-user.conf files. It turns out that one machine has a "~/.fonts.conf" file, which I've moved to "~/.fontconfig/fonts.conf". Strangely, the other one doesn't have "~/.fonts" or "~/.fontconfig/fonts.conf"!
I'm glad I found this bug report. I just upgraded two machines from 12.04 to 12.10 and only one of them was giving the warning, even though they have identical 50-user.conf files. It turns out that one machine has a "~/.fonts.conf" file, which I've moved to "~/.fontconfig/ fonts.conf" . Strangely, the other one doesn't have "~/.fonts" or "~/.fontconfig/ fonts.conf" !