is the Redhat / Fedora installer. IIRC, files that are suffixed with .anaconda are files that have been created by the anaconda installer.
I remember that you have to copy /etc/lilo.conf.anaconda to /etc/lilo.conf for lilo to pick it up correctly.
To answer your question: No, no difference in the contents of the file, but the file wont be used if not named lilo.conf.
Are you sure you are using lilo as your boot manager? I think Fedora defaults to GRUB and doesnt even offer to use lilo.
Hope this helps,
By the way, there is a very insightful posting
on the fedora users mailing list on the topic.