Why is 'Cool On' or 'Heat On' flashing on my thermostat display?

The flashing 'Cool On' or 'Heat On' message indicates that the built-in compressor protection feature is engaged. This prevents damage to the compressor by forcing it to wait a few minutes before restarting after shutdown. Wait 5 minutes for the system to restart safely, and the message will stop flashing once the safe wait time has elapsed. (Page 3)