What does it mean when 'Cool On' or 'Heat On' is flashing on the display?

A flashing 'Cool On' or 'Heat On' message means the built-in compressor protection feature is engaged. The thermostat is forcing the compressor to wait a few minutes before restarting to prevent damage from restarting too soon after shutdown. Once the safe wait time has elapsed, the message will stop flashing and the compressor will turn on. (Page 15)