[andrewas]

My machine has two firewire ports, of two different types.

When I wired them up, there didnt seem to be any preference as to which one went to which header, so I dont think the ports are supposed to behave differently in any way.

Possibly your aunt's machine only has the one port connected. Happens sometimes if the case has more ports built into it than the motherboard has headers. Also happens if the tech cant be arsed finishing the job. Might be worth taking a look, but if you only need the one port it shouldn't be a problem.