The red light is supposed to come on when you plug the transmitter into the charger. It indicates that the transmitter is being charged. One day I plugged my transmitter into the charger and left for work. My wife called me on the phone all flustered because the charger was flashing.
Nothing to be concerned about. It will continue to flash for a while after being plugged in. My charger is still using the battery that came with the CGM, which is about 2 years ago.