Deary me you're right, J1 = J3 and J3 = J1.
I latched onto the designations assuming that they would be a defined standard not left up to the whim of every PCB designer. I know you normally designate components in a logical progression across/down a PCB but with a standard all important components should be called the same thing by everyone and Arduino is arguably a standard.
You live and learn eh? Sorry for the confusion.
Rob