Is it just one quick flash on and then right back off again and not multiple flashes? If so, then it is nothing to worry about. Most, if not all of my decoders do this every time I power up the layout. I often work with microcontrollers similar to what these decoders use and this is normal behaviour. When the decoder powers up the internal pullups on the microcontrollers digital outputs will allow the decoders outptus to turn on until the microcontroller "boots up" and executes the code that enables the output drivers and forces the outputs to turn off.
What system and what decoders? Digitrax decoders will flash the lights if there is a short in the motor side. If all decoders do it, is there any beeping from the booster that would indicate a short?
--Randy
Modeling the Reading Railroad in the 1950's
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