Your security clearance screening has nothing to do with immigration. Security clearance is issued in order to facilitate access to privileged and confidential information, when necessary - such as your job. It might help with some aspects, but it depends on the type of information they will be looking at as part of your application. Will it be comparable? We cant know that.
I also believe that you do not have grounds to submit a complaint. Did you have contact with CSIS? Was your clearance revoked? Was a decision made based on CSIS provided information? If your answer to all of these is negative, then you have no base for a complaint.
CSIS, like any other government department, has its own process and timeline. Their primary mandate is national security! Security checks can sometimes take longer for some people, depending on the volume of verification required.
Scenario: Lets say you do submit a complaint. What's to say they wont take months to investigate your complaint. All the while, your application sitting and collecting dust, until they reach a decision. And when the decision is made, it will have take the same time as a regular check. A little bit of patience goes a long way. But as usual, its your choice.
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