Your background investigation is not run entirely out of FBI Headquarters. Much of the legwork, including interviews with neighbors, past employers, and personal references, along with scheduling of the polygraph examination, is coordinated through field offices local to where you have lived and worked. If your history spans multiple regions, your file may need coordination across several field offices at once, each working through its own caseload alongside yours.
The background investigation is often the single biggest source of timeline unpredictability, because it depends on the availability of people outside the FBI's direct control: former supervisors who are hard to reach, references who take weeks to respond, or records requests from other agencies and institutions.