CentOS uses both font systems and they use different folders: http://www.centos.org/docs/5/html/Deployment_Guide-en-US/s1-x-fonts.html
Red Hat Enterprise Linux uses two subsystems to manage and display fonts under X: Fontconfig and xfs.
The newer Fontconfig font subsystem simplifies font management and provides advanced display features, such as anti-aliasing. This system is used automatically for applications programmed using the Qt 3 or GTK+ 2 graphical toolkit.
For compatibility, Red Hat Enterprise Linux includes the original font subsystem, called the core X font subsystem. This system, which is over 15 years old, is based around the X Font Server (xfs).
On CentOS5/Redhat it seems that XFS gets its fonts from the X config file /etc/X11/fs/config which points to /usr/share/X11/fonts, and fontconfig gets its config from /etc/fonts/font.conf which points to /usr/share/fonts. By default neither font system sees the fonts from the other system.
Seems that RH wants to move to fontconfig but still has some things that use XFS. Why they didnt just put all the fonts in 1 folder and pointed everything there so that both font systems had all the same fonts is a mystery.