When topping-and-tailing trains with multiple engines, I'm finding the cab controls often don't sync. This is mainly an issue I've been having in my free-roaming sessions, but it has also cropped up during the 'Leaves' story mission. Once Gordon attaches to the rear of James' train, opening the throttle on James's cab does nothing. The way I worked around this is to set either James or Gordon to full forward on the regulator (the train stays still), and then disembark and move to the other engine, at which point opening the throttle starts the train off.
I had a similar issue with the Thomas and Gordon scenario, turned out that Thomas still has his breaks enabled and I had to manually turn off Thomas' breaks before Gordon could move.