Hey Espeelark,
Thought I would throw out something - I am reading the manual (that thing you read after you start ... you know - LOL).

The section for using multiple HC's suggests you give each HC a unique name (example HC1, HC2, Mike or Bob .. etc).

Then before operating make sure each HC is found under Acc's page, main page must be on to do this - read instructions ...

Maybe this will help in your situation ? Again - throwing this out there ...

Pages 7,8,9 talks about it, especially for use of the "Stop All" function, allows it to send stop command to all HC's as long as they are all talking with each other.

Atlas switches are DCC... cordial... at best.    I have a bunch of them on my layout and the biggest issue I have is shorting at the frog simply due to the design of the switch. They are dead frog design, but the opposing rails come so close together that wheels will often span the gap causing a short. Liquid electrical tape or simple clear nail polish will usually do the job.
As for powering them, If you happen to have an old DC powerpack lying around, just wire that up to power the switches. Quick & easy.

When my father-in-law retired, my Dad asked him how he was liking it. His response was, "I've never been so damned busy in all my life!!" 

Hi KPack,

How long of a ime "off-power" did the Rapido Mo'Power provide juice in the GP38? I'm seeing just seconds, and that's just with lights and the idling prime mover, no motion. I'd be surprised if it was providing 5 seconds of juice, I'd say more like 2-3 seconds.

I installed a LM-21S into a Rapido GP-38 with their keep alive, and it worked great.  5 minute install, including removing and reinstalling the shell.  Best install I've ever had.

The model runs perfectly and the keep alive works as expected.