You mention a reversing loop, but you also talk about three turnouts. Are you using a wye? It may be helpful if you post a diagram of your layout or at least the portion with the reversing problem.
It has been a while since I used a PM42, but I do recall having a problem similar to what you describe. I couldn't get it to stop, so I started using a different auto reverser and the problem went away.
Are you using powered or dead frogs on your turnouts? Whose turnouts are you using?
Wiring For DCC