I'm having the same trouble with my debian sarge distro and the latest ubuntu release.
Screen fonts display correctly in all apps but the following: xmms, xmule, audacity, alsaplayer, gmplayer.
I have played around with the X -dpi 100 setting, the paths to my fonts are user readable, since Scribus and OO.org can load them. It does not make any difference if I log in as root or user.
What can I do to fix this?
An example of the effect I get on screen is available here:
http://www.vademecum.net.pl/~auriga/zrzutekranu.png
Note how the icons on the desktop have acceptible fonts, as opposed to those in the xmms menu.
thank you
Arthur