When you switch to the Security tab and enable AutoLogin you have to select a blank entry from the user list and then re-select the user you wish to AutoLogin as. If you do not the settings are incorrectly written in the /etc/X11/gdm/custom.conf file, the entry for AutomaticLogin=<username> will be absent. Also if you later disable AutoLogin and just uncheck the box on the security tab only the AutomaticLoginEnable=true entry is removed from custom.conf the AutomaticLogin=<username> entry is left in the file. So to properly remove the entry you must first select a blank entry on the user list and then uncheck the AutoLogin checkbox.
As I understand it, you have two problems: 1. When enabling autologin, you have to select an empty line then a user for the username to get written to the file. Correct? This appears to work fine with 2.16.x, my username gets written fine. 2. When disabling autologin, you have to select a blank user, not just uncheck. Admittedly, the line is left in the file, but autologin does not happen (with 2.16.x), so why exactly is this a problem?
Does it work? Yes I suppose, if one wants to click between the custom.conf file and the gui to see what changes are actually being made. If the user has manually entered any of the AutomaticLogin values into custom.conf gdmsetup does not appear to parse them and show them as enabled. Re-enabling them doesn't create duplicate entries. However don't you think gdmsetup should accurately reflect what is actually in custom.conf? This may seem just cosmetic if the end result works, however as a person who builds LiveCD projects and everything is configured through scripts it is nice to have the end product (gui) reflect what has been manually configured in the build scripts.
I think that if gdmsetup doesn't properly parse manually edited custom.conf files, that it's a matter of upstream, and not for us. If it doesn't work with it's own edited files, that's a major failure, that needs to be patched locally. Could you please file a bug in http://bugzilla.gnome.org and post the URL here?
Paul, as requested above - if you can still reproduce this w/ gdm-2.18.2, file a bug upstream. This is not a Gentoo issue.
Closing, it's been 10 months. Please open a bug in Gnome's bugzilla as Jakub suggested. Thanks