ORIGINAL: vertigo72480

Futaba's mode two channel assignments are
Channel 1: Ailerons
Channel 2: Elevator
Channel 3: Throttle
Channel 4: Rudder

Look at your Futaba radio. From right to left are the trim adjustments. On the right side gimbal you have Aileron (Channel 1) that slides or clicks left and right. You also have Elevator (Channel 2) going up and down.
On the left side gimbal you have Throttle (Channel 3) going up and down, and Rudder (Channel 4) going left to right.

The trim switch layout matches how Futaba assigns their channels. Kind of like and arch going right to left in ascending channel number order. I came across this little mavel of engineering by accident. Knowing this little trick really makes it easy to setup an aircraft.

What it really sounds like, is you set up your servo connections wrong. The Tower System 3000 is made for Tower by Futaba, as Tower has a vested interested in Great Planes and Futaba. Change the connection of your ailerons and rudder at your RECEIVER to match the layout I gave you above, and you shouldn't have any more mix up problems.

This should also keep you from spending any money on shipping your radios back and allow you to spend it at the LHS instead.

Please PM me if you have anymore questions.