After realizing today that the installer 0.4 doesn't handle copying the backed-up custom.conf instead of gdm.conf, I wondered if catalyst was even creating the backup. It isn't. This is a Bad Thing(TM). I'd create a patch, but this fix is so trivial that it's a waste of both of our time :)
Why would we backup custom.conf? With the new gdm config stuff, there's no need for backing it up, at all. The only thing in custom.conf is the stuff to make it auto-login and such, the exact stuff we made the backup to avoid having on user's systems. This new behavior is actually good for us. The backup was only necessary for the older gdm.
Because custom.conf is in CONTENTS for gdm, so it (with our modifications) gets copied into the new install.
... For now, fsscript it out of CONTENTS or something... heh
I've added this to CVS now...
Fixed in 2.0.1