Repower up the system with nothing on the track like sugested. Put one loco on the track you know wont caust the unit to flash it's lights. If this works you unit is fine. Check the tender wheels on the loco that caused the short. These should have wipers on them. One side of each axle is insulated. Make sure the insulated wheels are on same side per truck and that the two trucks don't have the insulated axlws on both side. IE the forward truck should have the insulated wheels on the left side as you look at it. The back truck should have the insulated wheels on the right side. If not this will cause a short.