Red Squirrel
No Lifer
I wonder if the motherboard does not like the fact that the PSU is being turned on and the power switch was not hit so it acts differently? One thing you could try, is hook up the relay in such a way that it only turns on momentarily, then hook it up to the power switch header. Then it would be like turning on the computer normally. I can't think of a proper analog circuit for that off the top of my head, but I don't imagine it would be too hard to do. Another option is to use a microcontroller that handles the turning on of everything, so pushing the power switch turns on the microcontroller and it turns on the appropriate relays to turn on what you need. For the computer it would just turn the relay on/off once. To reset you would turn on the main power switch, but could also have a separate reset button.