I checked your site to determine what configuration you were using this jrok converter in but since you have quite a few projects listed I could not determine if you are using an arcade PS or PC PS and Jpac or Ipac etc.
Ah, that's because it's for my next project, so no documentation as of yet!

If you have more questions perhaps you could outline what is being powered and what interfaces are being used.
The next project will basically be a MAME cabinet, but I want to be able to play JAMMA boards in it too (I have a Neo-Geo MVS boardset already). So I'll be powering a PC, TV, various 12V lamps, 5V for an Optipac, and 5V for the Jrok RGB encoder.
Right now, I want to be able to use the TV in the Neo-Geo cabinet, since the monitor is non-functioning in it. So I guess for now - in that cab - I'll be powering the TV, the Neo-Geo PCB, 12V lamps by the coin door, and 5V for the Jrok RGB encoder.
To make it easy.. Use one PS (a PC one is a good choice). Most newer arcade power supplies are simply small switching supplies very similar to a PC supply but with less output capability. I was just trying to make sure that you were not connecting the jamma harness and the jrok to different supplies.
Why would that be bad if the JAMMA harness and the Jrok were on different power supplies? I guess I'm still not getting why this would be bad.