Funny you should say that, I've just got a Futaba T6XA. I've been using JR equipment for the last couple of years and this is my first Fubata. Last night I plugged everything in to test the system.
This is what I found:
channel numbers on the receiver, all servo's 'normal', Futaba 3004's
1. Aileron Left/clockwise
2. Throttle Up/clockwise
3. Elevator Up/clocwise
4. Rudder Left/clockwise

See something wrong? I tried two receivers, so it couldn't be that.... so I set up the dual rates and sure enough, the elevator rate switch affected the throttle servo. So, I took the back off the Tx and checked to wiring to the ginbals, all looked ok. At that point I was resigned to the fact I might have to send the Tx in.

Turns out that these Tx's can switch modes and it had been set up as (or inavertently changed to) mode 1!

BTW, my JR receivers have ail, ele, rud, thro, etc printed on the receiver and the Tx refers to the functions too, so I've never really thought about the channel numbers except maybe the channel reverse switches on the back of a Quattro but I forget what they are...