The Studio 540 mainboard may or may not be an OEM variant of a generic product. Typically the headers (apart from the front panel) will be standard, but in this case there seems to be an issue.
A possible remedy is to use a continuity tester (obtainable from an auto parts store) to determine if the pin assignments are standard. If not, you can rearrange the wires on the Firewire connector to suit.