Peter,
I had the same type of problem, auto play (Accompaniment) and the RT1 and 2 were playing a semi-tone apart. After spending hours searching for the answer I remembered a post on this forum that stated that using a improper pedal to trigger the slide can leave the note being played a semi-tone out-of-tune.

When I removed the pedal the keyboard it functioned properly.
You may have to initialize the keyboard, not sure.

Hope this helps, John C.