My son graduated C School at Dam Neck in April. His security clearance was completed just before he finished A School. To be honest, I shocked they waited so late to complete this. Apparently the investigator assigned my son's file had dropped the ball on a number of files and was fired. The new investigator was scrambling to get everything completed. Anyway, he appeared at our door unannounced. Talked with me for about 90 minutes. I had been warned by friends/family who had recently been thru this process to only directly answer the questions (like a legal deposition) and not to offer any additional info. Our investigator left notes on neighbors' doors and talked to everyone he could get his hands on.  Guess it all worked out.

My son is an officer who went to Intel School also at Dam Neck after OCS (Officer Candidate School.)   His background check was done before he was accepted to OCS.  The investigator talked to our neighbors. (Thank goodness we were able to give them a head's-up first that he wasn't in any trouble!)   Also went to his high school and talked to the guidance counselor and principal, and went to the local sheriff's office to see if they had any record on him. (Thankfully, no.)  They talked to two of his Boy Scout troop leaders, and I believe also one of his summer job employers, so it was a pretty thorough background check on our son.   

Seems surprising to me also that they are allowed to start Intel A school before the background check is complete !