Need to restore Fedora 16 from a backup

I am a newcomer, and I hope that someone will help me find out what is wrong, and learn how to do this.

I have been performing backups using f -> Administration -> Backup. The backup location is a second internal HD, NTFS partition. It creates about 50 files of the .gz type, each about 50M in size.

I selected back up of everything in the file system /, but excluded /media, /tmp, /home and Trash.

Today it was necessary to do a restore. So I used the same application, requested a restore to the original location. It said the system had been successfully restored. I did a restart.

Now, the system has not been restored to the same condition; many files I've found that have not been changed back. "yum history" still shows all the updates that had been performed after the backup.

And the system is unstable and almost unusable; the Application Launcher (f) is no longer available, and a number of things don't work. Something major is wrong.

Maybe we have to be running from a rescue/restore disk, and not from the system itself, that is being restored? Is there a way to recover and restore my system from the existing backup?

Any help would be very much appreciated.