Knee pain could be mechanical, your posture when doing these exercises could be leaving your knees damaged? You may need to have your balanced runners checked, maybe add some feet supports to correct the knee angles etc. It fixed my issue somewhat.
Glucosamine/ Chondroitin/ MSM is generally used when there is suspected arthritis. The supplement is used to help the body make more cartilage, and to reduce pain; in the knee for example. There is controversy as to how helpful this supplement is in improving arthritic knee pain, but some patients do report benefit with long-term use.
As you've had regular medical checkups and MRI without any findings, you may consider discussing with your doctor some next steps which may include: physical or occupational therapy, an exercise program, or wearing knee braces, to name a few. You may also consider some topical pain relievers such as capsaicin topical patches (Salonpas is one such product) applied 3-4 times daily when needed. A next step if topical therapies are ineffective may be to add Tylenol on an as needed basis.