Hi - I have lifelong migraines BUT when my ectopics started 6 years ago I certainly noticed an association between the occurence of ectopics and triggering of severe migraines - just think about what an ectopic is doing to the cerebral blood supply -making it erratic and pulsing. What is a migraine - contraction then dialation of cerebral blood vessels. I also noticed that when ectopics set off a tachycardia afterwards, then it would directly cause a headache and often migraine. Understanding headaches and migraines is a neurological specialty as is cardiology -unfortunately specialists often have very blinkered views! My suggestion would be to keep a headache/ectopics diary - maybe using one of the migraine diary sheets from the migraine charities - then you can present some evidence to a Dr.
Personally I have not experienced severe headaches with my ectopics. I do sometimes feel a headache if I get a lot of them close together over an extend period of time but it isn't severe. How may ectopics are you experiencing a day? I would suggest going and seeing your doctor to get the headaches evaluated. Take care. I hope you feel better soon. Keep us posted on how you are doing.