Third power functions train runs backwards, why? We have the passenger train and freight train, both run from a single controller - one through the red and one through the blue side. At Christmas we got the holiday train, and with the power functions kit coming back in stock with Lego, we just added power to it. 

Having set this train to red on channel 2, its forward is counter clockwise. Both trains on channel 1 go forward when the dial is turned clockwise! 

How do I reverse the controls of channel 2 without affecting channel 1?
There are little black switches on the train remote control which you can use to invert the direction.