It is quite possible that since you have to shift the modulation that you got a "Futaba compatible" Hitec receiver instead of the "Airtronics compatible" receiver that is the opposite shifted modulation. That's why when the buddy box trys to take over, the signals are reversed and the servos try to rotate 180degrees. I BET if you plug it all in to the Airtronics receiver and shift the RD6000 back to the correct modulation to match the receiver and the buddy box it will all work.

I have an older Airtronics PCM receiver that I tried to get working with my RD6000 and when I shifted it to PCM1 an got no response, but on PCM2 it responded, but not correctly. So I would only use a receiver that is the correct modulation type for your txmitter. Whereever you purchased the Hitec rxer from, you might try taking it back and exchanging it for one that has the reversed polarity from what the one you have is.