I've I've got you right, when you sit cross-legged one knee is up 45 degrees, the other is on the floor?
I would suggest you practice crossing the legs the opposite way and spend an equal amount of time both ways. Also when that knee is in the air you could prop a little pillow under it. It is much easier for the body to relax into something than to relax into thin air. This is a principle of yoga therapy. I know what you mean, this can cause a lot of tension and leg pain.
I will post a couple of suggestions for asanas to help with this later...gotta run now!