The second epidemic (in the fall and winter) was a combination of "camp fever" (diptheria), chronic diarrhea and "flux" (influenza).
At least this is what the chroniclers of the time wrote, but mind you that none of those diarists (at least the ones I read) were surgeons. I would like to read something from the medical department to confirm all this.
Camp Hope was said to be one of the cleanest army camps in the State at that time, but the sanitary habits of the soldiers made it very unhealthy. This all happened before germ theory was generally known.