Yes, I think you're right that the headaches could be from dissociating; a different kind of headache. But even with that, perhaps what you are experiencing is someone having a migraine? Have you tried migraine meds?
Attitude is part of this I think? I wish you could be more comfortable with dissociating, and allowing meditation to let what happens happen. When you become upset with the results, that probably adds to the headache dilemma? (((Hugs)))
If you're finding you're dissociating more, then you probably do need to slow down and reduce your activities. It might mean that there's too much going on for your system, maybe even going too fast in therapy etc, covering too much material or trying too hard to understand everything at once.
It's all ok: it's all you.