For some reason the system gives me a message:
Not exact look, but all the text is there. I get no errors, if I do Control-D it just repeats the message, if I enter my root password, it gives me the shell, and from there I can type "reboot" to reboot the system without any further messages. It's really annoying and I can't find any error in the logs. Any help would be appreciated.

You need to run a fsck on your hard drive. The command to issue is listed in the message it gives. It is possible that you might have to re-install but try checking the file system first.

I don't think you understand, the computer is working perfectly, I only get this message when I attempt to restart the computer from the gnome start panel. This has nothing to do with fsck. And in case you still aren't' convinced, I have already run fsck to ensure that it was not. The quoted msg in the first post the only message given, as I said I get no errors, it just drops gdm, and shows up in the console with that message. I enter my root password and manually reboot once again, and the computer reboots. Once again, this error is not related to fsck, the message may be similar, but I only get this error when I REBOOT the computer, not during the boot process, the partitions are perfectly fine and have no errors.

How exactly did you come to that conclusion? What command is mentioned?