He moves from his chair plenty in cutscenes and such. None of the other characters move from their respective spots on the Normandy either. So Joker never leaving his chair is not even close to being a tipoff.
I never went that deep into conversation with him in the first game. And then in the few cutscenes you see him up in the second game, I don't think I ever noticed him limping.
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~Halo There is no Crane, only Scarecrow!
http://img195.imageshack.us/img195/3739/scarecrowq.jpg