Neil.
I'm with Reiner on this one - sure sounds like a problem with the cable or back, but as I wrote you via PM, I'd first try some of the different setting configurations on the back and then in the camera section from within phase one. If that doesn't get it to see the camera then I'd try a different cable. I have noted problems tethering once I added the Leaf Aptus 12. Sometimes when trying to switch from the Leaf to the phase or hasselblad backs, things are just frozen once using the Leaf back. I have to shut down all the apps (LC, C1, Phocus) that use the firewire port and restart - sometimes I have to completely restart the computer. I sure you've tried all that, but thought since you also have the AFi-ii 12 that it would be worth mentioning.
Good luck!
Eric