I have knee pain but I already know the source of the problem. If it's something that's really significant, getting your GP to take a look might be a good idea.
Have you tried double jointed stirrups? They are expensive to buy but might be worth giving a shot. Not sure if in your case it would make a difference or not.
Because of my hip problems as well as my knee I have found that the stirrups that have more give, also cause a bit more general movement but it helps me absorb the shock the way I want it.
Not everyone finds it helps them. An idea to try out.