Sometimes allergies can be devoid of runny nose and watery eyes. I have severe allergies and take Zyrtec but there are still times that I will have an allergic reaction to something and just get the headache without the nasal drip or watery/itchy eyes.
It could be possible you are having mild migranes as well, they can be at the base of the skull and last for days and weeks on end. There's also a very remote chance you could be having spinal cord problems at the base of your skull around c1 - c3. It is more common however to have problems with the cspine just a bit further down. But it's a thought.

What I'd probably try is one of the OTC allergy pills like claritin for a few days or week to see if that helps any at all. If it does chances are you are having problems with allergies. If it doesn't help at all you may be having a migraine. In either case if it persists I'd get it checked out again.