it has to do with the muscles tightening and putting pressure on the eustachian tube. It's really annoying, isn't it. I've found that stretching my neck, not away from the side with the ear problem, but towards it and experimenting with keeping it there or massage will sometimes open it.
Ive just been doing exercise and have the same problem, so i was looking online for a reason and a cure.. All the stuff i have come across seems to point to the same thing.. air pressure. Every time you swallow, some air goes up the eustachian tubes and into the middle ear and gets absorbed by the membranous lining. But sometimes the tube gets blocked so the air inside the middle ear gets used up and this pulls the eardrum tight.. which is the pain.
Some people just happen to have smaller eustachian tubes than others. So when your exercising, you breath more air and swallow more and this can cause a blockage..thus causing the pain.
It is possible when you are running; you may be keeping the mouth closed and heavily breathing from the nose. At times, during this phase sometimes there is an increase in the pressure of air in the space behind the nose and pharynx, which may temporarily block your Eustachian tube. Try some different breathing exercises or you may try using some nasal drops before you start to run. This may help this unique complaint
Your problem is highly suspicious for Temporal Mandibular Joint Dysfunction (TMJ). Ear pain not associated with hearing loss during exercise, especially in cold temperatures, causes jaw joint area spasm, which is commonly felt as pain referred to the ear. Heat and sometimes a mouth guard similar to those worn by football players should solve your problem.