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Have you tried a different PCI Express* card in those slots, to ensure that they are working?
And have you tested your FireWire* card elsewhere?
I don't have another PCIx1 card to try in the mobo. Since the firewire card works well in the x16 slot I would assume that the card is OK. What is the likelyhood that both the PCIx1 slots are bad? Based on the block diagram in the manual, many other devices appear to be controlled by the same chip and they all appear to be working properly.