Configuration will not deploy if no profile is logged in

I'm preparing a major application upgrade configuration. The custom script config runs perfectly if the computer is on and anyone is logged in. However, I need to get it to run even if no one is logged into the PC. Is there an option that I'm missing?

Also, will Desktop Central wake up a sleeping computer with WOL? I'm having issues getting it wake up our laptops even though they're connected via LAN.

Thanks!