1) The Clone should not send power command since its power setting should be set to "no power button".
2) The Watch Analog/Digital Tuner activities should select the Clone as the primary device for both channel changing and the Display function. Add the the main device like a passthrough device using the activity add feature, and when it ask what input to use, select " "I don't need to set the input". If you add the main device any other way, it will force you to select an input. In these activities, you don't want the main device to send any input command - just the power command.
3) In the Clone adjust input settings, make sure you answered all the questions correctly.
4) Check the interaction of the database commands "InputHdmi1" and "Mode" in device mode. Are you sure the "InputHdmi1" does not reset the TV Tuner cycler to one of its 2 possible states? If it does, then you will have to use a different scheme (like the pseudo discrete sequence scheme instead of the clone scheme). You should NOT need to send additional Startup input command with the Clone method.
5) Does the database "Mode" command behave the same as the original remote TV toggle button? Like I said before, you may need to learn the TV toggle command from the original remote. You may need to learn it in RAW mode to prevent it from picking up the existing "Mode" command.