nscrbug sorry to hear that you are having problems. It sounds like you are referring to Posterior Knee Pain, and as you've already explained it maybe caused by too high of a saddle and the saddle being to far back, which are two of the causes of stress on the biceps tendon and Posterior Knee Pain. It may take sometime for the swelling to go way but it should get better as long as you've resolved the saddle high and aft issue, also stay away from steep climbing until you are completely healed, and if it does not get better you may need to take few days off the bike.
Deya



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