In the wake of the Snowden/NSA leak and more recently the Alexis/NAVSEA incident, DoD and other organizations are examining their procedures for granting security clearances. Also, Congress is set to hold hearings on the subject. PSC is trying to preempt Congress from beating up on contractors when the issue is more widespread.
There's plenty of blame to go around. The Navy itself may be a major contributor to the problem. While in the Navy, Alexis shot out the tires of a car belonging to construction workers who were parked next door to the house he was living. The Navy investigated and their report removed any reference to him using a gun. It merely stated that Alexis "deflated the tires on a construction worker's vehicle". Based on that characterization, the Navy granted Alexis a secret clearance. Later, he shot a gun into a upstairs apartment and by that time, the Navy had had enough. They released him. However, the Navy gave him an honorable discharge and the highest possible re-enlistment code.
About 75 percent of security clearances are issued to military and civilian employees of the U.S. Government. Only 25 percent are issued to contractor employees. Whatever gaps there are in the process of granting security clearances are equally applicable to all individuals seeking to obtain or retain a clearance.