Problem when running heater

I just purchased a 16' Eclipse Iconic 44.5 ft Toyhauler. When I turn the thermostat to turn on heater it starts up and everything is working fine. After a hrs or so if I turn the heater up my overhead rooftop a/c unit also comes on. Is this normal ? When it's on it just blows cool or cold air, the same time when the central heater is on. I have also noticed a noise underneath the refrigerator that sounds like a flapper for the heater moving back and forth. It is extremely loud and scared the **** out me the first time we took it out and used it. Can someone please chime in and let me know what the problem might be ? I'm pretty sure thatvthe rooftop a.c. shouldn't be coming on when you only have the thermostat set for the heater. Need help
Thanks Dan H