That simply shouldn't happen. Either something is wired wrong, or there's a bad component.
It takes an iron man to play with a toy iron horse.
MR did a section on the wye reversing in Dec. '06. You should check it out. It has diagrams and tells you how they wired the whole thing. Make sure all the components are there. Don't skimp out thinking that something won't need it if it's important.
Peace
Really need to know what type of DCC system and what model auto reverser is being used.
Martin Myers
My friend has a wye and uses Dcc, he uses a reversing module to change the polarity. That works fine but then he loses control of the loco until he unplugs his throttle and plugs it back in and then it aquires the loco again. He tried three different locos all perform the same. I suspect the dcc system loses com while the reversing module is switching. Is there a known cure?