I'm not sure this is the right forum, but I don't know where this should be posted, and I ride fixed.
I've ridden fixed for about a year and a half, after about a year and a half riding a singlespeed commuter. I've never been a skidder, always stopped mostly using my brakes. I've never had any knee pain, at all.
I just got a new bike, custom frame/geometry, got it professionally fitted to me, and my knees HURT, like ALL the time. It's nearly exactly the same gearing as before (48x17 versus 42x15).
I'd never gotten my old bike fitted, it wasn't custom or anything, and I never had a problem. Are there specific culprits I should be looking for? This is driving me nuts.