Almost sure that this is about wrong voltages. Check if the 'wrong' cabs deliver correct voltages, especially for 5V. Should be around 5.10. Too high will fry gameboards, too low will give boot problems.
Tip: never connect a PCB/Naomi to a power supply without checking for correct voltages.
It's either what Cageman says or there is something wrong with the USB cable or I/O board. I had an instance where I was getting Error 01 and everything was wired find. I checked the USB cable and that was the problem.