I'm not sure about this set-up exactly. I have seen where some electronics run hot. How they handle the motor draw is part of their design, and can be their weakness. There are recent boards released that want an external fan applied to cool them!
Maybe this (Sountraxx) example is driving the motor incorrectly? Are you running it on it's correct established voltages? which model are you using?
https://soundtraxx.com/product...gital-sound-decoders
maybe page 61 would help set-up the decoder to handle the motor better?