My knees were hurting again like 4 or 5 days ago, I took it easy, took 3 days off the bike, and I'm feeling a lot stronger / better now. I think it's a matter of muscle recovery to some extent, because the pain I had wasn't right in the knee but slightly above so I think it was muscular and not a joint issue. Than again I'll also be the first to say that while I know a bit about nutrition and the organ systems and all that, I can't say I know a lot about muscles / joints / fitness info besides things like what to eat before / after workouts and why...

Either way, MSM also helped my knees when they were hurting from improper fit, I posted a thread about it in nutrition and some skeptical old guys got mad, but my knees feel better and they can be damned for having closed-minds.