Wow. That is interesting. I just started riding fixed within the last week and I haven't experienced any of those types of pain. I don't know if it is that ever body is different or what, but I don't think I would attribute any of these to biking. As a matter of fact, riding fixed had an antithetical affect on my knees: the popping and grinding actually stopped which is contrary to what most people's concerns were.
But, you should definitely check here:
http://www.sheldonbrown.com/pain.html