I have a similar leg length discrepancy. I find that the saddle of my commuter bike is rotated a few degrees clockwise every time I ride it. It's a folding bike, so I'm adjusting it several times a day, but the result is always the same. The seatpost clamp is tight enough that the saddle doesn't drop. I'm assuming the leg length difference somehow puts torque on the saddle. Not a problem; just interesting.
Steve