Hi,
By the sounds of things npower have taken over the incorrect supply when applying for yours originally, if british gas have always been the supplier, they will be entitled to bill you for full usage since you moved in.
Your payments to npower should more or less cover their bill, and you would almost certinly get a payment plan from b/gas for the rest. You may be able to get some money off for them taking so long to notice if you push hard enough, maybe not..
I don't know if this would come under back billing charter or not to be honest, b/gas really should have been sending you bills if they were your supplier so you might have an argument there if the difference between what you've paid npower, and what they will bill you, is large.
Ask these guys for some advice
http://www.consumerdirect.gov.uk/