The SC is conducted by the DeFence Vetting Agency and comprises of a few factors. They will look at your credit worthiness, Check of identity, integrity and deliquency issues and finally the Counter Terrorist Check. The final stage takes the most time (the average, providing there are no significant issues is 120 days). The DVA and Rec Servs have been under remarkable strain due to increased departmental workload and other significant factors. The work both agencies do quite fracnkly is staggering and they work every hour to ensure the SC are completed in a timely fashion. However, this increased strain does put a bottle neck on the system so ultimately slowsthe process. An avenue that Rec Servs has and depending upon authority, they can issue a 308A. This is a certificate of understanding that the candidate completes acknowledging that the RAF is managing Risk by letting them in with only the basic clearance. You sign on the understanding that if the SC is retruned with a significant find then you could/would be dismissed from service.
Individual delays could be due to late submission of the Mod Form 1109, refs don't effect this as they are part of the BC and this is conducted at the AFCO (Identity, proof of address and Integrity - satisfactory Ref). Celtic surnames, overseas connections, scottish candidates (due to Disclosure Scotland) and Irish Candidates can also experience delays. Any undisclosed deliquency or descrepency can also effect this - compared with the Form 493ROA1974. The AFCO will be chasing this constantly so don't worry. I hope this is useful and remember I'm 'Here to help'