My guess is that it is referred pain. Your drop foot is likely causing you to walk differently that usual. The your altered gait is putting stress on your knee. Prior to havong my hip replaced my gait had become so messed up that it felt like my knee was going to explode. As soon as I got my hip fixed, and my gait returned to normal, my knee stopped hurting.
I am going to agree with kwarendorf (but I'm not a medical expert and also guessing!) because I immediately thought of the foot drop causing unusual stress on everything holding your knees together. If it bothers you enough, please consider talking to the docs and perhaps getting a physical therapy referral. There might be some simple exercises you can do to help with compensating through that knee. You sure don't want to make it worse.
I just read your intro and am always thrilled to find people who are on a therapy so sucessful it reverses disability. Going from wheelchair to walking due to Tysabri is quite the testimonial and I have heard it before.
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