Just bought a 6D and a third party battery for backup. I've charged the original LP-E6 with no problem. However, the third party battery didn't charge even when I've done the same procedure as written by the OP. I've exchanged it with another third party battery and same thing happened. Finally, I've just added a some money and get another original. However, the store where I bought it tested it both original and third party battery in a third party charger and both worked. I guess it's true that the Canon charger is doing some confirmation if your battery is original or not.
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