Not if you are getting a routine Secret/Top Secret DoD clearance....it is done by the DSS and/or OPM, whoever is in charge these days. Often it is actually a civilian contractor for the OPM/DSS. Other agencies use the SF-86 and other agencies conduct those background checks, like the FBI. The FBI does get involved in some military investigations, like Presidential Access programs, but not your average military clearance.
The context of the post you are quoting me from is me speaking to the urban legend, that often comes from GIs or ex-GIs, that their clearance, even their basic dime-a-dozen-entrance Secret, is what is causing the delay.
I submit that it's not the reason for Private Snuffy's or Airman Joey-bag-o-donuts' delay, and there is no connection between National Security Clearances, issued by any authorized agency, and the NCIC.
This proves to me that you are DHS operative.