@Commodore,
Just reading the M1230XA manual again and there's a note about its onboard clock. It says the clock chip on the board should be removed if you have a real time clock installed on the motherboard. Since your Delfina card fits a clockport, I assume you have a mobo clock (?). Sorry if this is a stupid assumption, but I know zilch about the hardware side.
Maybe this is where any posible timing problems are occuring?
You could try removing the M1230XA clock chip and the battery. It's the third chip from the left, top row as you view the board from the 'front' (CPU side)with the edge connector at left. Use a small screwdriver to pry it out of its socket.
Cheers, JaX