Duratrax intellapeak false charging

I got the new charger the twin pulse with the new IB4200 WCE batteries and Ive already chraged the batteries like 10 times so I dont think I have to break them in. But as soon as I plug them in sometimes both lights will start to flash and sometimes only one will? Why? One time it charged for like 50 min. and I checked the voltage and it was like 2 or 3 volts from the peak on on battery and the other was like a volt off?