I think the background check in progress means that the officer will review the information gathered by all the checks, i.e., police check, biographic, education, Medical, security, etc. and makes a decision on the application. For the case of security check, the security officials may recommend that an applicant is clear and there is no evidence or concern security wise. Then the officer may decide that the application can be approved. Or they may recommend that there is no major concern at the moment but additional investigation may be required. The applicant may be categorized as a low risk one. The officer may choose to approve the application but with a condition to have the applicant under some sort of surveillance. Ultimately, with all the gathered information the officer wil need to make a decision based on the available information. This is just my hypothesis on how the process might work. It could all be wrong.