The FBI conducted background investigations. Even for the military.
Later, OPM took over, under Bush the Lesser. Debacle city, as they were understaffed and the war ramp up required people with clearances.
Now, we contract that out (previously prohibited by law) and the contractor apparently dislikes encryption of data at rest.
Note the prohibited by law part, yet those who changed that law are "now asking pointed questions".
Just more panem et circenses.