I have very little doubt that Pataeus has had extramarital affairs. I also have very little doubt that it has very little to do with why he resigned.
How do you know? Adultery is a crime under the UCMJ (Uniform Code of Military Justice). If he couldn't keep it under the rug, he would have been forced to resign. If the wrong people found out about it, there wasn't going to be much Obama (or anyone for that matter) could have done to save his career. I doubt that the Administration would let him go down in flames or set him up; imo they will be hard pressed to find a military man with his pedigree that will be as amenable to their agenda.