If I wanted them both powered at the same time though, I think the second option you outline is schematcially the same as what a drew. The only difference is that I propose daisy chaning ground from all the controls, which feeds into a switch that selects between ground between the iPac and JROK. This would prevent both devices being controlled at the same time, right?
That approach might work on a single system that uses isolated grounds such as the X-arcade encoder.
- Each input group has an isolated ground.
- If you use the ground from group A with the inputs of group B, the inputs register as if you grounded the inputs from group A.
The problem is that your systems don't use isolated grounds.
- The IPac is grounded via the USB cable/shielding==>computer ground==>power outlet ground.
- The JAMMA board is grounded via JAMMA harness ground==>power supply ground==>power outlet ground.
Regardless of the switch position, the ground of one system provides a round-about ground path for the other system through the power outlet ground, hence the saying, "Ground is ground."
Of course, you
could use an 18-Pole Double-throw (18PDT) or equivalent relay setup to control which system's input each button connects to.

- It's a bit complicated and somewhat expensive, but effective way to switch inputs with both systems always-on.
- You wouldn't need the blocking diodes for this setup.
Switch ____ JAMMA Input
Ground ___/____/____ Encoder Input
Relay
If the diodes aren't needed I'll l leave them out (I'd need 36 of them..), but if there's any chance of damage to the JROK, I'll put them in.
The blocking diodes are a best practice and cheap insurance for your setup.
- The odds of damage are low (but not non-existant) if you try it without them.
- If you run into problems you can add them later.
Scott