Ok THESTRATCAT,

Here's what I think happened. You are set up on the MX 400 as its a mechanical set up. When you tried to set up your AXE, you had to program a new model number and then set up your swashplate to s-3. When you started programming this new model number, I'm guessing the MODE (or STICK # as the manual says) may have gone back to #1 by default. So, when you select model #1 (MX400) everything works, but when you select model #2 it has the stick backwards 'cause its still in mode 1.

copy-paste from manual:

Changing the 6EXHP stick mode
The transmitter may be operated in four different stick “modes” (1, 2, 3 & 4). The modes
determine the functions that will be operated by control sticks. Currently, the transmitter is in
“mode 2” and should be left in mode 2 unless you are an experienced flyer and have learned
to fly in a different mode. In mode 2, the right control stick operates the aileron and elevator
and the left stick operates the rudder and throttle. This is how 99% of Americans fly their
models.
To change the mode, simultaneously depress the MODE and SELECT keys, then turn on the power. The current mode will
appear on the LCD screen. Push the DATA INPUT lever up or down to change the mode. If a mode is selected that moves the
throttle control to the right stick, the throttle detent mechanism will have to be moved as well. This can be done by the
Futaba Service Center. (See page 2)