I have checked all the other pins and all seemed to be swapped out correctly...
What seems to have happened is my connector pinout was actually correct..
But electrically what I had labelled as pin one for example, was actually pin three electrically in the schematic.

Problem being while I labelled up the correct pins in the PCB part, and the correct pins in the schematic part and labelled up correctly, there was a third connection for electrically connecting the pins between schematic and PCB part,which I must have forgot to do (again)


As before, I will post the PCB file here (Hopefully later today) so anyone who wants to order them can do so.