HI Reuben, thanks for the post and nice youtube video on your website. People should watch this before commenting on your issue as it give an idea to the forces you are putting through your body.

I have to say that your history sounds like you have perhaps torn a structure in the back of the knee. Obvious suspects are the popliteus muscle (a small muscle in the back of the knee that assists unlocking from and extended (straight) knee. The wear and tear on the Wikipedia reference-linkmeniscus is probably normal for someone with your vocation.

As for a bakers cyst, was there a swelling in the back of the knee prior to this issue? It might be possible and often people don't touch the back of their knee that often (unless painful) so these can be hiding there unnoticed. All a bakers cyst is is a herniation of the knee capsule (like a bladder in a basketball) and the fluid pushed out through a weakness in the bladder causing a 'cyst' like appearance.

Often when a Bakers Cyst bursts the swelling goes away rather than appearing. So the fact that your developed after the injury does not really point to this. You might well have torn your posterior Wikipedia reference-linkcruciate ligament which often tears the posterior capsule and releases the swelling down the calf all the way to the ankle/foot.

The best overview I can suggest is that the fact you cannot fully straighten the knee with a flexed ankle means that something cross the back of the knww and the ankle is involved. This would point to the muscle of the calf or popliteus. That is if you can also straighten the knee fully with the ankle pointed.

If you can't straighten the knee in sitting with a pointed ankle then something more internal might be the issue. Unfortunately in this case you are going to need someone to have a 'hands-on' look at the knee. I am sure there's plently of willing people in NZ to assist.

Best of luck