There was a great article in the New York Times about how the USDA is simultaneously trying to get people to eat more cheese while telling them that saturated fat is bad for them.
I was trying to think of a good analogy before but just came up with this: imagine if the Minerals Management Service (theoretical regulator of the oil industry) was in charge of setting the fuel economy standards for cars and trucks.
The Minerals Management Service (now the Bureau of Ocean Energy Management, Regulation, and Enforcement) is a pretty good example of that as it is. It's in charge of enforcing environmental regulations and such for oil companies, but it's also in charge of collecting oil and gas royalties for the government. This is part of why oil companies have historically been so friendly with it -- they are somewhat interested in avoiding regulation, but they are even more interested in minimizing their royalty payments.