Joel, I'm not sure what actice exercises you are doing, but I would encourage you to try giving some more time to "Beginning of the Universe" and if your knees can "work through" the standing aspect, "Breathing with the Universe". What has been your experience with these exercises or with "Seven Steps of New Life"? I have personally experienced pain relief with these exercises. I see them as well as the sword fingers work in Level 1 as a foundation for Level 2 work. Keep developing your own practice, including the Self Concentration exercise which provides an opportunity for each of us to work with our own energy blockages.
I have found my knees respond with pain to a severe squat, but are okay during and after standing qigong practice if I just slightly bend more knees.
It actually sounds to me like you are getting some pretty decent results with the examples you shared. One thing that popped into my mind when I think of people who don't respond is Chunyi Lin's point that some people such as engineers do not get benefit from this information healing. One might say they are concrete or process reality in a black or white way. To put this in another way, some people will likely not respond for reasons that have nothing to do with you.
I think you are getting pretty good results with others. Good luck in working with your knees.