I'm by far not an audio guy so I'll tell you what I know, tell me if I'm wrong. Once I get my facts straight I'll be able to say if its an actual PC issue hardware/software.
It's to my understanding that the M1 can send a pulse to turn on amps and such. So how it should work, to my understanding is this: IGN on, 3 second wait, Pulse the system board, 3-5 second wait, Pulse the Amp. The amp now draws power until another pulse is sent to tell it to stop drawing. If this is the case use a meter to see that pulse.
I know for sure that minlogon does some crazy things, including not shutting down your PC. I got frustrated with it and decided to not impliment it. Why? My boot up times were not really changed after I nLited windows and put it on a CF card maybe the same will hold true for you. This case is especially relevant if you plan on implimenting EWF, since writes are now to RAM.
If everything works normally under winlogon then I'm guess the M1 must monitor the state of the PC checking to see when it has shutdown, when its shutdown it then pulses the remote line.
I dunno just throwing stuff out there....