I'm back into cycling after not riding for 40 years. I'm 58 and suffering from knee pain at night as well. I am o.k. while riding the bike which is setup correctly and I am trying for more RPM and less torque. The pain radiates to my foot and hip and I find I have to lay flat on my back to get relief. A few times in the AM I could barely put any weight on my right knee when I get up. I have a doctors appointment next week so we'll see what they say. Hopefully not arthritis but like you, I find it strange that there is no pain while actually riding. I also have been experiencing NPS which has slowly been going away as I get used to riding again and also some pain in my left testicle. I don't think the two are related but they might be. We (wife and I )started out gung ho on riding and I think we pushed too hard too fast. In the meantime I'm riding shorter rides and not doing any sprinting in hopes of not causing further damage. I'm hoping slow conditioning of the knees and muscles that haven't been used in a long time will alleviate the problem and getting my sit bones accustomed to the seat will reduce or eliminate the NPS and testicle pain. You sound like an experienced rider and your bike was already setup correctly and you are used to it so while we have similar knee issues, they may be very different problems. I did a lot of damage to my knees by working as an alpine ski instructor for almost a decade and skiing on every day of the season. Let us know if you find out what your issue is and I will post if I get any meaningful diagnosis/prognosis from my doctor