If the system worked once, and nothing was changed, I doubt it's the installation. I strongly suspect operator error caused by adding engines incorrectly. If the situation were on my layout, here's what I would do. I am here addressing DCS locos only; leave the TMCC alone for now
1.Disconnect the 2 wires from one TIU channel, and connect them to a3-foot section of track (I say 3' because I have Gargraves track lying around) that is not a part of the layout. I would turn on the PH180 that feeds that channel, and not turn on any other transformers.
2. Reset all of the remotes.
3. Use ONE remote to turn on the channel feeding the separate 3' track. Leave all other remotes turned off
4. Place ONE loco on that section.
5. Add that loco. I will want to come in as some ID number, but force it to be added as ID #1. When successful, use the remote to shut down the engine.
6. Remove that engine from the track section, and place another on the section.
7. Add that loco. Force it to come in as #2. When successful, use the remote to shut down that engine.
8. Repeat the above to add the remaining locos, each with the next highest available ID.
9. When all are added, use the Loader program to clone all the other remotes. If you have special desires on the softkeys for each loco, make those changes on the remote before starting the cloning process.
10. Reconnect the TIU channel you've been using to the layout, and try operating.
I recommend the above based on issues I have encountered when engines have lost or garbled their IDs and wouldn't add. The garbling came about if power to the track was cut (as by a circuit breaker opening) when a PS2 battery was dead or a superconductor had not yet charged engouh to run the shutdown procedure.