Kneel on the mat and put a cushion on your calves and sit on it. Use a 'meditation bench' consisting of a slanted board on 2 legs. Put it over the calves as you kneel on the mat and then sit on the bench. This may be remedied by using more cushions. Generally the legs must be in a symmetrical position - what one is doing, the other must do.
Most people are also more comfortable sitting with their hip joints higher than their knees.
Sitting past one's physical endurance so that the mind becomes focused on the physical position instead of its real work.