The problem could lie with where the loco connects to the tender .there could be two brass leaves that connect to the tender post if these are not correct then a short can occur .have you replaced the 4 fishplates where the tender stops ? Can you connect your controller to the track where the tender stops.?
I would suggest you have a short circuit at some point causing the select to reboot itself . You may have to do a little trial and error as to where or what is causing it. First off could a loco be shorting on the front bogie from time to time ?.
Hi Can you verify you have a DC voltage on the track ? And it varies when you turn the controller up and down .I would suggest leaving the loco's off the track until DC is verified . Then check the loco's for mechanical lock up .check the loco's with a battery if poss.