I have the same thing! When I asked here, most people told me there was no way it could be related to Lucid Dreaming, but I believe otherwise...

Sometimes the pain is at the base of my skull and down my spine a bit, even.
Other times, I will feel dizzy and have a slight headache. Sometimes I dont get them, though. But it never happens with normal dreams, only lucids.

Perhaps it has something to do with you exerting your brain,
Or maybe from when your body goes paralyzed in sleep...
Perhaps your spine is getting pissed off lmao.

I'm not sure what the case is.
Its caused me to basically dabble in Lucid Dreaming
Instead of practice it everyday like before. (for that, and other reasons).

I don't know what advice to give you though, since you very well can't ask your doctor, unless he believes in Lucid Dreaming XD. Even if he/she did, I doubt they'd have enough info on it...