Just to contribute to the timeline here, a colleague of mine submitted his SF86 back in August 2016 for a Secret clearance for a military contractor. It took about 2-3 months before I received one of his letters covering his background check (Since I was his previous manager).
Since then he hasnt had any contact or followup that I know of, which is very unfortunate since hes been out of work since then. He has recently told me that another colleague of his took 9 months to get clearance for the same position.
It seems like such a substantial impact on the these people waiting to get to work, I hope this all gets gets cleared up ASAP.