Left knee pain in front, right in back...
 

I just cant seem to find the correct seat height. One knee says move it up, the other move it down. Pretty sure my legs are not different lengths. The fitter didn't say anything when he was setting the bike up for me. Only seems to bother me after 25 miles or so, anything less and I don't notice it.

Anyone else dealt with this situation?

Knee pain could also result from your cleat positioning on your shoes. I used to have a lot of pain/stiffness in my right knee... adjusted the cleat and goodbye pain.

Before the adjustment it would hurt before and after riding, but while riding the pain miraculously vanished after the first few miles. Now I am pain free all day. (I feel like a commercial, sorry)