The knee problem looks to be related to the JMCrKneeBend morphs on the thigh and shin. The left most knee here has the thigh JMCrKneeBend set to -1.0 and the shin JMCrKneeBend set to 1.0. The middle knee has them both zeroed. The right most knee has the thigh-shin joint edges highlighted in yellow. The JMCrKneeBend morphs affect the way these edges line up. You may be having cross-talk issues?