The NYT has a great story highlighting a recent disagreement between the Food and Drug Administration and the Obama Administration over whether movie theater would have to post how many calories a box of popcorn has. The FDA though of it as a policy health issues - as it is supposed to - while the administration thought about the political fallout.
They provide a list of other areas where they disagree.
This is a great was to get a handle on the limits of presidential power over the bureaucracy, especially when the policy goals of the latter conflict with the political needs of the former.
