I admissions that would preclude you from employment in an agency block your chances from getting a military clearance? Do investigators from another agency turn up those admissions?
It seems that yes, agencies (such as the CIA) share information from pre-employment polygraph examinations with other federal agencies. See the message threads, CIA Shared My Sexual History (https://antipolygraph.org/forum/index.php?topic=2493.msg17578#msg17578) and Do post polygraph statements get shared? (https://antipolygraph.org/forum/index.php?topic=3378.msg23465#msg23465) Depending on their nature and recentness, such shared admissions may or may not lead to the denial of a security clearance by another agency.
Interesting. I had found this link and was starting to think the opposite. The agency in question for me wasn't the CIA so it makes me wonder. What an annoying thing.
https://antipolygraph.org/forum/index.php?topic=3008.msg21236#msg21236