Tinstaafl hit the nail on the head with his answer. All things being equal, the difference in the fuel burn is the parasite drag from the extended upper deck. When compared to the original upper deck the extended deck has a little bit more drag.
One of Boeing's designs for the -400 was a completely extended upper deck. That resulted in slightly less drag than the original upper deck. However, one of the requirements for the -400 was to have it fit in the same footprint as the classic. If the upper deck was extended completely, a new wing would have to be designed. As it was, the winglets were added to handle the increase weight without increasing the footprint.
