It seems to be acting on the extmute_off "player" command after it has turned off and switching back on again.

You didn't say what device you had connected to the mute line?

I'm guessing that whatever device that is, it's changing the state of the mute line when you turn off the ignition (or shortly thereafter). So hijack dutifully sends the IR command to the player when it sees the state change. So the player is doing what it's supposed to do: Waking up out of standby mode when it receives an IR command or a button press.

Try setting your standby timeout to something really short, like 1 second or maybe even 0 seconds (dunno if that's possible). If the device (whatever it is) changes its mute line state slowly enough, maybe that'll fix it.