What does the flashing 'Cool On' or 'Heat On' message on my thermostat screen mean?

The flashing 'Cool On' or 'Heat On' message means the compressor protection feature is engaged. This feature forces the compressor to wait a few minutes before restarting to prevent equipment damage. You should wait 5 minutes for the system to restart safely without damage to the compressor. (Pages 46 and 63)