An Irish (atco) colleague of mine submitted his through the company at the same time as the rest of us and had no problem.
My understanding is that to submit an application for processing, you have to either be employed, or have an offer of employment, and that the company will be your "sponsor", otherwise the security service will not be able to issue authority for you to have access to the pertinant areas at your home base.
I am not sure about a Disclosure of good conduct, as far as I know, the requirements of this are encompassed by the Disclosure Scotland form, again the employer should be able to verify this, but the information you have to provide on the disclosure form covers almost every evenuallity.
I suggest you take it up with the people who hopefully will be employing you soon.