Barry gave the Fix, Here is why (It's in his book, along with a ton of other useful things).
When you power up the layout, the DCS TIU briefly sends a watchdog signal on all the outputs.
All Protosound 2 and 3 engines look for this signal for a few seconds when they power up.
If they see it, they stay dark and silent, waiting.
If they do not see it, they assume the layout is Conventional and power up.
Pressing Startup makes them shift to Command mode with no changes in what they are doing.
I believe Pressing Shutdown will also put them in command and shuts them down.
Then again, I haven't had to do that in a while So the memory fades.
Love the Big Steam Trains!