What transformer are you using? Secondly are you running the conventional locomotive at 9 volts using the transformer throttle or the remote? What channel are you running through (Fixed or Variable)?
A electronic or magnetic/hydraulic circuit breaker between the power source and TIU inputs is an excellent idea if you aren't using a modern transformer (like a Lionel 180W Power House brick). Another option is fast blow automotive fuses with a rating of 7.5 or 10 amps.