[Poohbah]

My experience: it would take something VERY serious for the chaplain to break confidentiality. The only incident of a chaplain running to the CO I ever heard of in the USMC involved a guy who (a) was starting to experience auditory and visual hallucinations and (b) was guarding a Special Ammunition Storage Facility.

[El Gato]

"Special Ammunition Storage Facility" == Nuclear Weapons Storage Facility, most likely. Although sometimes other weapons are termed "special", it usually means nukes.