I had a secret clearance which got me a position in a major relay communications center in Panama while in the Army. I don't know to what extent the military goes to do any background investigations but I suspect none since I had guys working for me who were given a choice by their judge to either go to jail or volunteer for the military.
One weekend I was the E-5 in charge of the center while my SSGT was off. I noticed a red light on one of the incoming message banks from a station on the Atlantic side of the canal. The red light indicated that a Top Secret Flash message was coming in over the teletype bank, which was very irregular since the particular circuit the station sending the message was using was not rated for Top Secret message traffic.
What made it even worse, I didn't have TS clearance to even handle the message myself. I was then required to contact my NCO due to the security breach as well as the station commanding officer and get them on site ASAP. Because the message was still in teletype tape form, I never even got to read what it was all about.........LOL!
The following morning, Monday, I had to go to the CO and file a report and by the end of the day I had a brand new Top Secret security clearance......LOL!
I had a TS/SBI with SCI. Spent about 4 months on AFI at Keesler while the background check was being performed. I PCSed to an AutoDIN facility where I had to pass thru 3 cipher lock doors to go to work. That was late 80s. The Air Force took security VERY seriously. ANY odd incident would get your clearance pulled and an investigation. And yes, homosexuality voided a clearance. I was in the day room watching Family Of Spies, the mini series about the Walker spy case. There was a crypto trooper in there that mouthed off, correcting something said in the movie about KG-84s. He got his clearance pulled the next day...