Yeah play around with it, but it's actually the DMAC card that's kicking it to turn on through the motherboard standard front panel header. I guess it's just designed as an always ON type of system and if it shuts down for any reason turn it back on. It makes sense from an arcade perspective.
Those options might effect it. Maybe number 1. Let us know if it does, it's not something i've ever really needed.
The problem is, if you get it to stop kicking itself on, how will you turn it on then? You'll have to hard wire a switch to PW SW on the FP header on your motherboard, just like a normal pc.