It could be because of a physical or functional asymmetry. You might be dropping one hip (functionally shortening the reach) which causes the other leg to have a functionally longer reach (as compared to if you had 2 legs of measurably different lengths). So, for posterior knee pain, you might need to lower your saddle a smidge and maybe turn the nose of the saddle slightly away from the side that hurts to try to balance out how you're sitting. These problems can develop over time, because it could take a while for all the muscle imbalances to develop and everything that would lead to pain.
Another thing to keep in mind besides your saddle position is taking a look at your crankarm length. My pelvis gets out of alignment easily. My left SI joint hardly moves while the right one slips out of whack. My left leg is my dominant leg, though I have strong and weak muscles on each leg (stronger quads and gluteus maximus on the left, stronger hams and gluteus medius/minimus on the right). A lot of it is due to many years of being functionally asymmetrical. I can work on my alignment to help some.
A while after I got my bike, I started getting posterior knee pain after doing a fair amount of climbing (though I used to do those same rides with my less fit self with no problems). The pain was worse on the right. My initial bike setup was pretty relaxed..saddle a bit far back, bars fairly even with the saddle. I moved the saddle forward. I noticed an increase in power, but I couldn't get the right knee happy. That made my neck hurt, because now I was too squished in the reach. I got re-fitted, and they moved my saddle farther forward and my bars way down. I then had to move the saddle almost uncomfortably low to get the right knee happy, and then it still wouldn't last when I'd hit the hills. Finally, I found a shop that noticed that my bike had been built with the wrong sized crankarms for that frame size. They were too long. It was only 2.5mm off, but that made all the difference. I got new crankarms installed and I haven't had posterior knee pain since.
I do still run my saddle a bit lower than some people recommend, because when I'm doing a hard effort, I will have more heel-drop than average (and thus more extension of the knee). It is still set up where I can spin with a more neutral foot position comfortably. I also have my saddle slightly farther forward than most, and that position has allowed me to sit more squarely.
I'm not saying you should rush out and buy new crankarms, but if you keep working on your fit and still have problems, that might be something to consider.




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