From what I've read (limited research at best), the "second wind" is an adaptation phase by your body. Basically you have to cope with your inability to use muscle glycogen as a fuel after a certain point. You've used up a certain type of fuel and you get tired. Then your body adapts and utilizes other components to energize you. Your heart may decide to step it up a bit, for example. So now there's an increase of blood flow to the muscle compensating for a decrease in muscle glycogen. In addition, serotonins and other pleasure / pain killing chemicals release as your body experiences hardship. Et cetra, et cetra.
The general idea is that your body is an adaption machine, and as it uses up one source of energy, it will find another (after a slight pause). = Second Wind.