Just reviving this thread form the dead, but I found exactly the same 'problem' today when I got my first set of rudder pedals - this was flying the UH-1H but I think the same argument applies. It was the pedal animations that sold me on this 'reversed' pedal issue. I was fighting against a muscle memory that was a false assumption my brain had made.
I've gone from relatively competent using a wheel on my throttle to complete beginner using pedals. Time and practice will heal this, but an interesting insight.