I found a workaround, if you run the script as a startup script (Project Settings - Plugin -Python - Startup Scripts) it executes and renders the queue as expected.
So what I did is to make a .bat file wich copies my .py script into the startup script location, then it starts unreal. Unreal runs the script on startup and renders the shot. After the rendering is done the .py startup file gets deleted.
Had some issues quitting unreal after the rendering is done so I run a parallel script lisning to the CPU usage and quitting unreal when its done rendering.
Some hassle to setup but it works for now untill I figure out a better way to do it.