I don't know but I really think the investigation and granting of security clearances is situational, like any other bureauocratic enterprise it tends to get the answer it wants. This is just based on my experience which is now 10-15 years old, but it's what I've got. I had a TS/SCI clearance in the Navy which was preceeded by several lower clearances before that. They did do a little bit of digging but not very much, one or two people mentioned 'the G men were around asking about you' but that was it. Meanwhile several of my college buddies went on to become civilian engineers working with DoE and DoD and needed the equivalent of a Secret clearance. They got put through the wringer, that is, the background investigation was a lot more thorough than mine or most of the other Navy people I knew. I can't demonstrate it but I got a strong hunch that it was a case of 'you're now in submarines and we really need more submariners, so we won't look too hard lest we find something we don't like'. Same for radar and electronic warfare guys, or several other specialties in demand at the time.
My hunch, can't prove it but I smell this happening, is that FBI investigations of political people going to high office (say US Reps. and Senators, and highup political people in the Executive branch) aren't going to be the full Monty that say a civilian electrical engineer moving over to General Dynamics is going to get. "I'm sorry but Dilbert here smoked pot in college and didn't tell us about it, no design work on F22 interior lighting for you". On the other side it would be "Oh, Mr Obama, you hung out with a preacher who preached "God Damn America", you've had a lifelong fascination with communism, and at least one of your mentors is a former terrorist bombmaker. No problem, here's the operations schedule for SEAL Team Six and I need you to approve this operation for Delta Force".
I hope they have some means for controlling what I see as a conflict of interest in these things too. I mean, suppose you're an FBI agent doing background on Obama or one of his bestest pals (ha ha like suppose Obama wanted to appoint his bomber buddy Ayers to some .gov job requiring a clearance) and you find something, how long do you think your career is going to last if you actually find some disqualifyng dirt on the newly elected Pres or his political pals?