Gaiba, it seems to me that if on 1 ocassion you have a positive result and at the 2nd ocassion a negative that there is a possibility of a trapped nerve as binmath suggested. at least something is trapped (likely in between C0-C1) otherwise you would have had twice the same response. (Or the cause is non biological)
What I would like to know is : what sort of pain, referred pain where referred pain. How about posture of cervical spine/ head and in general. Mobility of spine, antalgic posture.
The information you supplied is not enough to diagnose.
on your second question: A way to mobilize could be by giving the patient a resistance (F2 on a scale of 5 as if you meassure musclestrength) against the direction you want him to move his head e.g. rotation to the right you give a slight resistance on the right cheeck (in lying) with the other hand you can palpate than all the vertebrae to see which one doesn't move.