Mountain biking has caused me ongoing knee problems for several years now. It has caused me to question everything:
Knee issues have also prompted me to stop mountain biking and road cycling all together for extended periods of time, up to a year.
My primary frustration in trying to figure out the solution is that my discussions with highly trained Orthopedic Surgeons (my Father was one) has left me almost as confused as attempts at self diagnosis online.
Online research, including internet forums, leaves you with the idea that your knee problems are coming from some sort of short-term bike fit inefficiency or poor training methods. Younger doctors will stray toward this opinion as well. Whereas Old-School Doctors like my Dad would focus on long-term wear and tear over many years. One side has a more popular solution and the other has unpopular reality.
A wise person, as I try to be, will attempt to put the two perspectives together: I have been cycling for many years, which is going to cause long term wear and tear on my knee joints, ligaments, cartilage, and muscles. NO MATTER how properly my bike was fit or how healthy my riding technique. But having said that, it is fact that bike fit and technique will undoubtedly determine the severity of that wear and tear. Another reality that every aging cyclist needs to accept is that youth masks a whole lot of future cycling problems.
So what is causing your knee problems and how to fix them?
The knee is the most common location for overuse injuries. It's most likely your knee problems are chronic -caused by long-term wear and tear / overuse-. It's unlikely you're going to be able to entirely fix the problem in the long-term, but it's perfectly reasonable to think you can deal with the problem in a way that allows you to continue cycling.
So, as a chronic knee pain sufferer, I offer this opinion: you're not getting any younger so you need to try harder to be a better cyclist:
To conclude my post, I will offer my strongest opinion: you're problems are caused by overuse and your seat is too low...