Re: unusual seiza problem - pain in BACK of knee
I had something similar. Had some arthroscopy done to my knee, slower recovery than I would have hoped for but I am about 90%.
I understand my issue to be my quads. In seiza, my butt generally does not make it to my heels. I am trying to get serious about addressing this. I have been doing squats with very little weight on the barbell, trying to go as deep as I can and do a high number of reps. Two or three times a day I try to sit in seiza for an increasing amount of time, and I try to hit the foam roller once a day too. Progress is pretty slow so far.
Make sure you get your doctor to give you an MRI - you can have lots of issues with meniscuses that don't show up on an X-ray.