Re: unusual seiza problem - pain in BACK of knee
It took me quite a while (years) to be able to sit in seiza with my bum actually resting on my ankles - as opposed to being suspended in mid air. Take your time about this stuff, and as recommended by others, don't overdo it as you can injure things - it's a challenge to learn the difference between pain which is just discomfort, and pain which means you are injuring things. Trust your intuition, and if in doubt I would err on the side of safety!
I find that the exercise furitama in seiza (hands clasped in front of you and being shaken up and down - but with an imaginary pebble between palms and with wrists and arms as relaxed as possible) helps a lot.