Hay Oscarman

Occasionally post surgery you can have an increased local inflammatory response and/or irritation in your local tendons / tendon sheaths and/or increased arthritic pain. However, I believe the anti-inflam gel / rest would have helped, and it is likely that with high impact exercise (running) you would have experienced pain earlier than the next day and redness/heat/swelling.

If you put your leg out straight, keep it relaxed and get someone to move your patella sideways / up down etc. then do the same movements with some strong compression (make sure they move the patella as far as it will go without being sadistic of course ). Does this hurt? cause similar pain? click/clunk? etc? Let me know! Sometimes PF problems can be overlooked even if it is "tracking" properly.

I completely agree with Gcoe though, get a therapist to assess you for a full diagnosis. It could likely be patella tendonitis, patellofemoral pain syndrome etc.