I am waking up every day with bad throbbing headsches at the back of my head. I have a known Chiari malformation. Could this be the cause of my headaches?

See a doctor. The headaches could be caused by your malformation and I think you should have a scan again. I would advise you consult your neurosurgeon.
Possibly yes. Get examined by a neurologist, preferably one who specializes in headaches.