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receiver problem

I am new to drones and trying to build a small drone. I have connected FS-R6B to naze32 rev6.I have a FS-CT6B transmitter. When I connect the flight controller to cleanflight configurator, the bars in receiver section move as I move the sticks on my TX. but when I disconnect naze32 rev6, the motors don't respond to my TX. It only responds when controlled from cleanflight. Even when I disconnect the flight controller, then power it on with 3s lipo, the receiver's light blinks once and stays on when the TX is switched on, which shows that a connection between RX and TX has been established. Then why doesn't the RX responds to TX? Please help