If you think about it, the remote starter has to tell the vehicle that your foot is on the brake with the "key" in the ignition and in the "start" position, then the "run" position to start it and keep it running. I would think it's done with software control and data these days, but if it's still done with relays simulating sensor activation, I could see the "run" relay being bad.
Be aware that your code scanner does engine codes, but there's a more advanced scanner that the dealership (and some indies) have that can also scan chassis codes. They are not standard codes but are specific to each manufacturer.
When the Corvette's braking ECM died, my scanner told me almost nothing (the dash info center told me more!). The indie shop had the GM scanner, and in less than two minutes told me exactly what was wrong.