People in the past have speculated they were getting more potassium than with their previous diets, or an allergy to sucrose (or another ingredient). One person was actually suffering caffeine withdrawal, as he gave up coffee at the same time as starting Soylent. Not a lot of consensus, since you know you are not dehydrated.
What I did gather, after reading five different “headaches” threads, was that most people’s headaches diminish inside a week. I take from that that headaches are a way some people adjust to altering their diet somewhat drastically.