The first obvious question is, well, why was the first study wrong? It wasn't. The biodiesel production process has changed and even though the 2007 study "extends to the energy required to manufacture the farm machinery used to produce soybeans" (according to a National Biodiesel Board release), we just get more energy from biodiesel today than ten years ago. Increased soybean yields, less herbicide and reduced energy needed to crush the soybeans means more energy in the final calculation. Get more details from the NBB and get ready to update your talking points.
[Source: National Biodiesel Board via B100 Fuel]