Could your cleat have twisted on the shoe?
How about your saddle height? Any changes over time?

I had bad knee pain a few years ago. Convinced myself I'd messed it up while backpacking. It got worse and worse. I was hobbling about. Went to the doctor, got the MRI.

Doctor said, no cartilage problems, but try some stretches. Like these:
http://www.youtube.com/watch?v=_ur0Y...eature=related

Told me to do some spinning on the road bike. I got some better float pedals, and stretched a bit, spun a bit, and quickly got better.

Tried mountain biking again. An epic ride had triggered the seemingly degenerative condition months earlier. Guess what? I could no longer tolerate the position my cleats had been in for several years. Played with the angle, and bingo.

I don't know if what you're experiencing is anything like what I described, but nobody will argue against playing around with your cleats if you've got pain.