May or may not help, but I had a similar issue once before.
What ended up doing was booting from the DVD and setting the start up disk (just like you already have done).
Then reboot. Once booted off the hard drive, I set the start up disk again and rebooted. From then on it worked fine.
In my case it was actually the drive starting to fail so not too long after that everything went to hell.
I believe it's also possible that the battery on the motherboard maybe bad. You can try replacing that as well. (someone please correct me if I'm wrong on this).