Admin preferences not sticking.

I don't know what's going on, but my admin preference for login items aren't sticking. I have several apps (FileMaker Pro, Daylite, iTunes) as login items if the server has to restart. Each time I restart the computer, iTunes has the agreement screen like when you first install it, I keep having problems with Daylite preferences, and Filemaker Pro won't seem to launch the databases (I use an applescript application to launch the FM databases).

I tried removing all of the login items except just one app, restarted, and they all loaded again.

I made sure that the option in the system preferences general tab to close all windows when quitting was checked.

No matter what I do, all of the apps keep launching and keep doing so with issues.

Any ideas?

Mac Mini Server

Mountain Lion Server 10.8.2