I have the service manual, and the info is in there - Doh.
Basically if you want the CD drive, Digital board and MPC to work in harmony.
The jumper on the PC I/O ADDA board needs to be in the "SET" position.
The jumper on the Digital I/O board needs to be set to the "SHORT" position.
Don't forget the 2 cables that go from the CD Drive to each board as well.
So if you DON'T have a CD Drive but you have the digital board I think it is safe to assume that the jumpers should be in the opposite position, like this.
The jumper on the PC I/O ADDA board needs to be on the 2 left most pins not "SET"
The jumper on the Digital I/O board needs to be set to the "OPEN" position.