I had the same thing, used to get a pounding headache when doing exercises that take the piss. Physio couldn't fix it and it got worse the more he manipulated it. Got to the point where it got unbearable, so I had an ultrasound, brain scan, blood pressure test and other crap tests the doctor around the corner from work sent me to get.
So I finnaly took a day off work and went to the family doc, who quickly diagnosed that, under stress, physical or mental, especially both, the tendoens / muscles that run from top of my scull down the back of the head and connect to the neck, inflame, tighten up and press on all the nerves, feels like a sledge hammer to the back of the head. He perscribed celebrex and told me to catch it early, when I feel it comminmg on, I pop a pill and tilt my head back and massage the back of the skull to loosen them up. Hot pack works instantly. Do not tilt head forward to "stretch" them, makes it worse, not pain wise, the ache lasts longer. He also recommended accuputure to fix it properly, but I never went.
I still get it sometimes, but it doesnt worry me as I can quickly manage it now, at one stage I was convinced that if I dont stop training my brain or a blood vessle in it will explode. It's funny it didnt feel like muscular pain, just a thumping headache I was convinced was comming from the inside of the skull rather than the outside.
From experience I would recommend a visit to your trusted doc and ask him about this before you let any physio mess with your neck.
Good Luck.