Have you confirmed the Reverser outputs on J2 and J3 Jumper positions are correct?
J2 – Reverser output to the reversing track. Use the screw terminals connected to J2, 3-4. It has parallel outputs for multiple loop connections if needed, J2, 1-2 and 5-6.
J3 –Programming jumper. J3-2 to J3-3 is the operating configuration. J3-1 to J3-2 when connected at power on sets the reverser to enter the programming mode.
J6 – Sets the current trip level when CV49=0. CV49 default is 03 which will set a trip current of 3.81 amperes if no jumpers are installed. If J6-2 is connected to J6-1 and J6-4 to J6-3 is open, then the current trip is 1.27 amperes. If J6-4 is connected to J6-3 and J6-2 to J6-1 is open, then the current trip is 6.35 amperes. If J6-4 is connected to J6-3 and J6-2 is connected to J6-1, then the current trip is 8.89 amp.
J7-1 and J7-2 are the auto/manual reset input. If the connections are open, the breaker will automatically try to reset. If the terminals are connected together (like a SPST toggle switch or a N/C push button switch), then the breaker will remain off after a short until the connection from J7-1 to J7-2 is momentarily off.
J7-4 to J7-3 Is the Inrush booster enable jumper. When the jumper is installed, the breaker will use a turn on algorithm that is designed to assist low power or overly sensitive boosters in starting high inrush current loads. It will also assist low power boosters such as the Zephyr and the NCE Power Cab to re-start difficult loads. When CV53 is zero, the jumper will enable/disable this function. If CV53 is a non-zero value, then the boost function is enabled regardless of the presence or absence of a jumper.
Is anything bridging the gaps at the other end of the reversing loop. A similar thing happened in one of my reversing loops when I parked a loco across the gaps at one end of the reversing loop. When I tried to run another loco into the reversing loop at the other end it shorted and stopped. As soon as I moved the parked loco off the gaps, everything worked fine.
I was also told by the manufacturer of the AR unit to have at least a 1/16" offset in the two gaps isolating the reversing loop from the rest of the track.