Not having ever installed Di2 myself, I'd just go back and follow the Shimano tech doc's, particularly the Dealers Manuals, and make sure everything I did is what they say. Read all the little sidebar notes in them and make sure you understand what all the pictograms are showing you.
What does the vendor you bought these from say? It might be you need to take it to an authorized Shimano shop. I've had to take mine in once only to be embarrassed that my battery was indeed not charged despite knowing that I'd put it on a charger a few days before.
Not saying at all that your battery is not charged. Just saying that taking it to someone more experienced and putting up with some ribbing and embarrassment will teach you something. Or, perhaps you and they will find that there is indeed an issue that requires a replacement component.