I have this same problem with Fedora core 1 and mozilla fonts. the version of mozilla (1.4.1) which came "packaged" with Fedora is fine, but if I download and install any later version, the fonts are crap and there's not the same choice in the "edit", "preferences", "appearance", "fonts" menu.
I can only assume it's something to do with the installation directories the fedora version of mozilla uses. Bits of it are installed all over the place like /usr/lib/mozilla, usr/bin/mozilla. but if you install the tar ball from mozilla it installs everything in the same directory.
I'm starting to find this kind of thing pretty boring to be honest and I can't find any solution to it. It's one of the reasons why even tho linux is a superior platform for servers, the desktop stuff is pretty mich a "geek's toy". Maybe it just depends on the distribution and how the distributors chose to install things, but it's just so hard to get answers to this stuff - OK if you want a hobby I guess...