Firstly, I re-installed FCP, and now the problem has manifested itself.
FCP 6.03, OSX 10.58 Dual G5 at 2.5Ghz, 5G Ram
Although I can digitize with the Pro Io with Capture Now, it will not acknowledge the deck at all.
a) I made sure the DSR-40 was in REMOTE mode
b) RS-422 is firmly connected between aja-io and DSR-40 DV deck
c) Set up the RS-422 correctly in device setup Sony RS-422, 2 channel audio, LTC+VITC Kona Serial Port
(this seems odd, as this is an aja-io), 29.97 hz, drop frame
If I edit this, this is the only option Kona serial