The MODE of your controller (TX) is basically what control axis the TX assigns to a particular stick movement. Here's a table from Futaba's website ( http://www.futabarc.com/faq/product-faq.html#q760 ).



The MODE that your TX is set to determines which control is operated by which stick. As you can see, if your TX is operating in MODE 1, but the simulator is interpreting in MODE 2, you would have some unexpected control movements.

Good Luck,
d.tipton