@O.P.: When you walk, which direction do your feet point? Do your knees always point in the same direction as your toes? If you jump in the air (just a regular jump, like you're playing basketball and taking a jump-shot) and then keep your feet exactly where they land, and then move your legs in (using your hips, keeping your ankles and knees locked) so your ankles are lined up below your shoulders, what angle would you guess that your right knee is pointing (with directly, straight in front of you being 0-degrees and anything to the right of that being positive-degrees). Is your left knee making the same angle, except in the opposite direction?
This really seems like a femoral/acetabular anteversion issue, causing hip abductors/adductor issues. I just had my legs reconstructed due to excessive femoral retroversion (I walked like a penguin), and I am in your exact situation. My hips/glutes/hammies/quads/etc. had atrophied to such an extend that I still (over 18 months after my last surgery) can't stand up from a sitting position using just one leg, and that's ALL due to still having weak hip abductors/adductors...
So if I had to guess, I'd say you need to work on your hip abductors, adductors, and hamstrings. Stretch them out several times per day dude...it sucks, BELIEVE ME, I know...but it needs to be done or you won't be able to sit cross-legged.
One test you can try out is this: sit down on your couch. Try to maintain a 90-degree angle at your knees. Now, lift one foot off the ground, and stand up with the other one. You *should* feel a massive activation in your hips. Those should be the muscles that are too tight, and are preventing you from sitting cross-legged (if my theory is correct, anyways).
Hope I was able to help you out buddy!
--Brian