Found this quote in another thread. This would explain why my 4 pin connector is not being used.
Originally Posted by deepsrd
AUX with 6FL:
The AUX (again 4 wires)is connected to the 26pin connector on the combox from the centre console. FActopry fitted 6FL comes this way.. When you code the 6FL to your CIC, it will then deactivate the direct AUX and will get the AUX from the combox via the MOST.