Check what your default run-level is by looking in the file /etc/inittab
You should have a line which reads:
I suspect that you have a 3 instead of a 5 though if you say that your X isn't loading up. Also, make sure that you have a sym link in /etc/rc5.d/ that points to the script /etc/init.d/dm - that's the graphical display manager script that starts X.
It's strange though that changing this in the MCC doesn't work.