Assuming your system IS DCC, and that it doesn't shut itself down due to a hidden short, then any problems you have are in the decoder...most probably. I doubt the base command station or throttle is the problem with scrambled bits somewhere. If the system powers up, and doesn't immediately shut itself down, then your wires are fine. If you have isolating gaps, really in AC the polarity doesn't matter providing you don't have a conflict with one side or the other coming into contact with 'itself' either via wire or rail and connectors.
Therefore, you have altered the decoder(s) somehow to all move in the same direction and not be able to reverse. I don't know what could cause that, and will let experts on inadvertent MUing or specific CV changes help you there. Mostly I wanted you to know that, since DCC is AC current, the direction of movement imparted to the drive mechanisms is dependent on the decoder...only. It is different in DC where polarity does matter. It cause the rotor to actually reverse its direction of rotation.