A couple of thoughts.
Our JH3 unit does not have the iLink Firewire option, but if yours does, you may want to check and see if there is a menu option which switches the machine control from iLInk to 9pin. Our DVCAM deck does have such a menu and you have to pick between 9pin and firewire for control. As you are going HD-SDI you'd want 9pin.
2.) The back of the deck has a "remote in" 9 pin connector and an RS-232 connector. The one you want to go to the Kona card is the remote in 9pin.
3.) If its not that, then its probably a device control setting.
Mike Klinger
Tree Falls Post/Clonetown
Los Angeles