That is quite interesting, con you detail how you do e that?
i think the powerCC website has instructions to add an extra power supply.
basicually what i did was get a pcb mount psu that would fit where the hdd was ( as i use sd/compact flash devices these days rather then mechanical drives) and make a pcb with a relay on it and some connectors to attact to the system
what i did what solder to the back mains power sockets and ran those wire to the relay (switch side) then to the new power supply
basically depending on if you have a 5v or 12v relay you then wire the other side of the relay (the coil) that is used to energize (turn on the relay) to either the orginal analgue boards 5v or 12v rail (i used the wiring harness and attached to the red 5v wire.
so what happens is that when i turn on the back power switch it all works like normal. you click the soft power button on the keyboard and it turn on the both power supplys at the same time. and shutting down the computer turns them both on. i run all my 5v rails though the new internal psu, the 12v still comes from the original analog board but considering that most of what i have running uses 5v, theres not much load on the 12v rail so i wasnt worried about that.
since then ive gone and done a Takky mod and run 6400 board in there and have no issues.
one other thing to check is the solder on the crt neck board. remove the back metal plate of that board and reflow/resolder all the yoke connections.