After upgrading my i386 redhat 6.1 machine to Redhat 6.2, the xnaim rpm overwrote my compiled version. After I removed the rpm and tried to compile the source, the xmkmf command failed because it couldn't find my XFree libraries. The files were there in the write place, however xmkmf couldn't find them. It all compiled fine when I used an included Makefile with the right paths
Upgrading a system will replace all files not marked with %config (true for all executables in a Red Hat distro). Look at the spec file for xanim to see how Red Hat builds with xmkmf. Otherwise, I don't see a bug here. Olease reopen if I'm wrong.