I agree.. the cross member, you're speak about can get spun around from it's original position and I believe that is what's causing the tangled webbing/strap. If one actually removed their soft top completely then chances are that cross member can get twirled around. There are points on the soft top where the fabric either snaps in, or velcros onto the tube frame. Also.. if you have the sunrider option this can complicate things even more.
Although this video doesn't show that cross member, it is a good how to based on the JkU's soft top take down.
In this instance, the cross member should go forward as to ally tention to the webbing towards the rear frame support. In other words, if the webbing isn't taunt, then something's wrong.