When the Rx light starts blinking, it means the Rx lost power at some point. You can duplicate this by turning on your Tx, then plug in your heli. While everything is bound, unplug the heli battery (leaving the TX on) and plug the heli battery back in. The Rx will start flashing to let you know it has lost power.
Needless to say, this is bad. I wouldn't run the batteries under 3.7 volts per cell. If you can do that, your batteries will last much longer.