The reason I just joined this Health Board is because I'm looking for a solution to the same problem! I don't think mine is as serious as yours but my ears, especially the left, pops non-stop when I'm running! It starts as soon as I get warmed up so I think it has to do with temperature and I guess pressure. It doesn't really hurt but it's really annoying. So, now you know you're not alone with this problem
I hope someone has a solution!