Hey schultzie. It is very difficult to say without seeing you perform these exercises. However, I reccomend you start doing lots of overhead shrugs to prevent scapular winging.
When you do regular barbell shrugs do you seem to have any issues activating your trapezius muscles?
I used to get knee pains when I did lunges. I was a lot weaker with the movement than I wanted to believe, and I thought that the squat had greater carryover to the lunge than it did. I know that in my case the knee was straying inwards and this caused problems - but again I cannot determine if your form is good or bad.
It might be that you hurt your knee with some lift ages ago and it hasn't healed. In any event I reccomend getting some knee wraps and using them after a generalized warmup to keep the knees healthy.