A little bit of progress (or not!) on this tonight.
I read (specifically here: Z68 Extreme7 Gen3 will not detect 3way sli! :( ) that populating Slots 1, 4 and 6 somehow causes the card in slot not to work. The GTX 670s are in slot 1 and 4 while the sound card is in slot 6, I had the same configuration when I had my CrossFireX setup, but this was fine.
I removed the sound card and placed it in slot 5, the PCI bus the GTX 670 was trying to access changed from 6 to 4 but still came up with the same error message.
I then removed the sound card completely, and moved the 2nd GTX 670 from slot 4 to 5, and booted into Windows (I also removed the SLi bridge as the gap is too big to use it). This time, no error messages in Device Manager, but it was using a generic vga driver. I updated the driver, and it now recognises it correctly and appears in nVidias control panel. I could use this for PhysX if I so desired.
I then moved the 2nd GTX 670 back to slot 4, but left the sound card out and the SLi bridge, but to no avail, the error message has returned!