@Leesureone did the two PCIe cards have the same USB cable layout, i.e. did the cables line up the same way in the motherboard header, usually on the bottom row of the header plug.
I have a number of different PCIe adapter cards from different manufacturers that have different 9-pin header cables. A couple of these don't line up and connect to the same USB port, when the cable is plugged in to the same header. I have had to change the Internal port so the new BT module works, when swapping a couple of the cards.
Each row of pins in the 9-pin header plug aligns with a specific USB port. So if the cables are in the bottom row in the header plug they will work only with the bottom USB port. Same goes for a cable plug where the cables are aligned in the top row of the header plug.
The issue comes when you have a cable that works in the header with the cables connecting the bluetooth module to the bottom USB port. Then switch PCIe adapter and cables and the second cable has the cables set to work with the USB port in the top row. The Bluetooth won't work in this case, not without first changing/activating the top USB port from the motherboard header.
When configuring our USBPorts.kext or USBMap.kext we would naturally only activate the USB port used by the Bluetooth module, the second USB port served from the header connector would be disabled/excluded from the kext, so as to keep within the 15 port limit.
