Well, the thoughts on a 12V problem were right on track.
I decided to pull the EMS control panel back out and look for loose connections. While I was at it, I thought I'd check the 12 volt fuses in the box next to it.
In the process I just barely bumped the F13 fuse marked furnace/roof AC. When I did that I heard the EMS relays clicking.
I "bumped" it a few more times and every time the EMS would power up or down.
Turns out that is the fuse that supplies 12 Volt power for the EMS. The terminals that the fuse plugs into had apparently spread over time and any little vibration (like that big diesel motor 3 ft. away) would cause the fuse to lose it's connection.
Ten seconds with a pair of needle nose pliers and all appears to be well!!