Nutrient composition of milk vs. home-made kefir
It could just be the difference in milk sources. Different cows, receiving variable types of feed, produce milk with varying nutritional content. They probably only tested kefir using milk from one or at most two sources. In comparison, the figures for normal milk could be drawn from hundreds of dairy farms across the nation.

I would expect there to be changes in the carb/protein/fat content of the milk, as well as vitamins produced/consumed by the kefir.  Specifically, the carbohydrate level should be lower from lactose being digested into lactic acid.