Throttle and Roll connections

First build guys and have a problem! Here is my setup! Multiwii 328p flight control board! FRSKY D8R II PLUS.Taranas XPD Transmitter. I have uploaded the Arduino sketch to the FCB I have made sure the sketch has the 328p defined in config h and also the setting in def h as from the net .It was all uploaded without any red errors!I have also bound the receiver to the transmitter ! I have double checked the connections between FCB and the Receiver and they appear correct! ok now the problem? ....... when i run GUI the throttle and the roll connections appear incorrect I have throttle to channel 3 and roll to channel 1 so when i power up the Taranis in mode 2 my throttle is on the right and not the left? when I switch them over the throttle then works on the left as it should but i think there is a mix up somewhere? any ideas guys?

Hi mate how are you swapping them,also when you set up transmitter did you set up as aero ( quad is set up as a plane) .
Did you by mistake set up as mode 1 not a mode 2 model