I posted this in a same subject thread about a month and a half ago:

"I'm no physiologist but I'd venture to say it's because your body (namely your connective tissue) wasn't used to it [why knees will hurt after a fixed ride]. Pedaling forward and pedaling backward (or resisting) may use the same muscles/CT, but doesn't use them the same way or in the same proportion. If you go out and rage, then suddenly apply a crazy amount of back pressure to joints that aren't up to the task then that's going to happen [knee pain].

I spend a considerable amount of time in the squat rack and see stuff like that happen all the time... you get some dude who jumps in there who can rep 315, 10 times (which means they *should* be able to rep 405 at least once), then they stack up 405, lower and bottom out; but if you give them just a little bit of a lift, past the point where most of the stress is off the CT [around 90 deg] and onto the muscle, they'll lift it just fine. Some of the newer sports medicine lit that's come out in the last few years highlights the higher percentage of injuries related to CT in professional sports over the last 10ish years and theorizes that it comes due to an increase of steroid usage because while steroids help your muscle tissue recover from micro trauma really quickly it doesn't do so for your connective tissue and the weakest link is always going to break first and if you don't give your CT time to recover properly, it's gonna be that. "