During the course of our healing we have experienced that in people who do a lot of meditation, headaches can be explained as follows-
During meditation a lot of energy flows into the body through the crown chakra but the nadis( energy meridians) are blocked hence this energy gets stuck up in the head area, cannot spread to entire body; resulting in severe headaches.
In many people the Earthing/ Grounding chakra is blocked, extra energy received during meditation cannot flow down to the earth, which again results in headaches and strong sensations at different chakra regions.
As for pain in Ajna particularly, it can result from cords coming to that chakra or can also be because of chakra energy disbalance even if no cord.
When cords come to any chakra/ body part they can really drain away your energy
To heal you we will have to check your aura and chakras.