I get headaches too from being dissociated. Ive been told that this is normal and one of the symptoms of having DID that most people with DID have. my psychiatrist told me there is no medication that will take care of this. he told me the only thing that will help is my learning how to do grounding stuff and relaxation stuff so that when I notice I am starting to get upset I can do them BEFORE I end up dissociating. If I don't dissociate I won't have headaches. So I have been working with my therapist and doing research here at the library on grounding and relaxation stuff and have been using them and it works for me. The less I dissociate the less I have been having headaches.