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I think that's what's happened, giving it a proper stretch out has seemed to do the trick, hopefully it'll help with the movement as well as my knee's been crap for years now... mine was a buggered when I had an arthroscopy, the surgeon had to cut out torn cartilage and suggested my ACL fix as well. One of my mates has gone through the same as me, seems like playing football at a young age isn't always the best.
Girlfriend had the suggestion of trying some yoga as we can do it in the flat (and do it for free via Youtube) and my knee pain has pretty much disappeared completely after a few nights. I used to stretch before and after a ride, but doing yoga stretching is a lot more controlled and has seemed to have done the trick for now. Not saying it'll be for everyone, but might be worth giving it a bash to see what happens.