Some of this is creative bookkeeping. Note that the raw energy values given in tables in these reports show an energy in/energy out value close to one. Not too good.

To improve this, something called "energy credits," is used, i.e. assuming the byproducts of ethanol production (distiller’s dried grains with solubles from dry milling, corn oil, corn gluten meal, and corn gluten feed from wet milling) can be credited against the energy required to produce substitutes for these byproducts. The benchmark usually used is the energy required to produce feed and such from soybeans.

Or to put it simply, if you wind up with a load of corn cowfeed at the end of your process, you get to add the energy to your plus side that it would have required for a farmer to grow and produce this cowfeed another way, like from soybeans.

Whether this is really valid or not is doubtful, but this is the method used to get those great numbers from the reports I looked at.

Now in the case of Iogen, I could not locate anything specific about their net gain figures...if you have a link, please post it. However, I could see where some sort of new catalytic process might result in less energy being required to produce the ethanol compared to more conventional methods.