From the TMCC troubleshoot guide:
THE LOCOMOTIVE CAB LIGHT
IS FLASHING:
THE LCRU2 CAN PROGRAM THE LOCOMOTIVE TYPE: STEAM
WITH OR WITHOUT RAILSOUNDS, DIESEL WITH CAB LIGHT,
WITH OR WITHOUT RAILSOUNDS, AND DIESEL WITH STROBE
LIGHT, WITH OR WITHOUT RAILSOUNDS.
THE LOCOMOTIVE TYPE IS SET AT THE FACTORY BUT CAN BE
RESET IN THE PROGRAM MODE. CONTACT LIONEL SERVICE FOR
THE PROPER SEQUENCE.
Did you try the "hard rest" for that loco JD?
TrainMaster Command Control operations
Reprogramming your locomotive to restore features
If your locomotive is unresponsive to your commands in the TrainMaster Command Control
environment, we recommend that you follow this procedure to reset your locomotive. All
factory default settings will be restored when you reprogram the locomotive.
1. Slide the Command reverse unit switch to the PROG position.
2. Plug in and connect your Command Base.
3. Place your locomotive and tender on the track, then power up the track.
4. Press ENG and enter the locomotive’s ID#.
5. Press SET.
6. Press ENG and enter the locomotive’s ID# again.
7. Press AUX1.
8. Enter 1 for this particular locomotive.
9. Turn off track power and wait ten seconds.
10. Slide the Command reverse unit switch back to the RUN position.
At this point, your locomotive has been reset. Restore power to the track and operate the
locomotive as usual. Be sure to use the ID# entered in Step 4.