Modeloldtimer
What CSX Robert said is more than likely what is happening. You are getting a short where the siding is connecting the two sides of your oval. In order for you to get it to work right... if this is the case... would be to cut gaps in the rails at both ends of the track that is connecting the oval. You would then have to give that section of track its on set of feeder wires. This is were it get kinda complicated.... You will need to find a Double Throw, Double Pole (DTDP) switch to use as an Auxiliary reverse switch. Here is a picture...warning I don't use paint well.
While the train is in the middle you flip the switch that way when you exit the rails are the right polarity....I hope this helps.
Brad
My Atlas GP-38 had a jumper that you swiched when you wanted to run DC.
I think it varies on the Protos. I think they would run on DC. I remember at least one of my Pk2's that didn't like DC much, though.
Chip
Building the Rock Ridge Railroad with the slowest construction crew west of the Pecos.