Npower can only back bill you 12 months. However, they are able to track exactly how much you paid by comparing your bank details to the meter no etc, they have transaction nos for every payment you have made.
Exactly the same thing happened a while ago with my gas account. Basically your meter has been "transposed" (mention this word to them). As long as you can prove your meter no, identity etc, then they should be able to get it sorted over the phone.
It's a case of applying the correct meter no to your account and an up to date read. As i said it's incredibly easy for them to sort. So, contact them and get this done. If they are still giving you hassle, simply threaten them with Consumer Focus. If they still fail to resolve, get in touch with Consumer Focus and they'll help sort it for you.