For what it's worth I had pain in the back of the knee a few years ago. It got worse over the course of a few months. In particular I could sit in seiza for extended periods of time, but it hurt every time I tried to stand up after
being in seiza. I eventually went to see a sports medicine specialist who diagnosed it as a problem with my popliteus:
A few weeks of good massage and (medical) acupuncture improved things tremendously and I haven't had the problem again since.
I certainly wouldn't presume to say that you're having the same problem; but I can't say enough good things about going to see a sports medicine doc when you have long-term problems!
Definitely get it checked out.