My wife has a similar experience if she spends too much time in water on the surface. It tends to make her sea sick. She doesn’t get motion sickness while on boats or once submerged and it does not include headaches.
The headaches do sound more like a CO2 problem associated with skip breathing. It could be brought on by how you attempt to control your buoyancy instead of skip breathing using shallow exhales. You may want to concentrate on doing just the reverse. Use more complete exhales and shorten the inhale. This way you can maintain the same buoyancy but rid yourself of the CO2. Watch your breathing cadence. You shouldn’t allow yourself any breathing discomfort trying to keep the inhale short. Use counting your breath cycle until your have reprogramed yourself to the new pattern naturally. Slowly count to 5 for a complete exhale, pause but do not stop before a slow 3 count on the inhale. First rule of scuba does still apply never stop breathing but use control to make sure you rid yourself of CO2 while maintaining buoyancy control and you may be surprised to find this will help your sac rate.