Description of problem:
I've just installed a Fedora 13 system on a blank disk from the DVD media (and updated it from the network).
If I "modprobe" a module, it says:
WARNING: Deprecated config file /etc/modprobe.conf, all config files belong into /etc/modprobe.d/.
The file /etc/modprobe.conf exists and is blank on the new system. I'm not sure who created it, but I didn't do it. :-) So it would save a message if the install process didn't create that file.
I just did a default install of F13 and anaconda did not create a /etc/modprobe.conf file. Perhaps you have a package scriptlet that attempts to do something with this file and creates a blank new one if it's not present?
Sorry for the noise - it turns out to be system-config-network (bug 589593).
*** This bug has been marked as a duplicate of bug 589593 ***