Flipper is an IR remote control and requires direct line of sight.
Sometimes a user will point Flipper away form the devices, resulting in one device that turns on or off while the other is off or on.
The first solution is to modify Flipper so only the TV turns on and off:
1. unlock Flipper: press and hold ADD until the light turns solid, then enter 956;
2. press and hold ADD until the light turns solid, then enter 999.
3. check your STB to see if your STB has a standby mode.
If so, make sure this is turned off. See the two articles on Dish and ATT.