I may be able to shed some light on this, not sure. What distro are you using? On mandrake ( and possibly redhat, can't remember ) i have observer the following:
abiword installs its own fonts in /usr/share/AbiSuite/fonts/. Is this line in your /etc/X11/fs/config file ???
My fonts went rubbish in all my apps because of these abiword fonts, but after i moved the /usr/share/AbiSuite/fonts/ line to the _end_ of the list of font locations in my /etc/X11/fs/config file everything worked out - i suppose doing that meant that mozilla et al would find the other fonts first, but abiword could still find its own fonts.
hope this helps.