I gather that security and background checks are different processes.
A security check consists of ascertaining whether or not an applicant has a criminal record, is likely to be a terrorist threat, etc. I am guessing that the visa officer who reviews an applicant's file looks at the police clearance certificate(s) he/she has submitted. But assessing the security risk that an applicant may or may not pose to Canada may involve more than just reading police clearance certificates. I don't know what else the visa officer does to fulfil his/her duties in this regard.
When a visa officer does a background check, he/she satisfies him/herself that the statements that the applicant has made about him/herself (name, family members, employment history, etc.) are true.
Although I've called them separate processes, I imagine that background and security checks sometimes may be related to each other. For example, I can visualize a scenario in which the visa officer discovers something odd while he/she is doing the background check, and that motivates him/her to do a more thorough security check. That is just a hunch on my part, but it makes sense to me.
Apparently the background and security check phase of the process can take anywhere from a few months to over a year. (That's not counting the time that the file spends in the queue while it's waiting to be reviewed by a visa officer.)
Background check is done by visa post processing application with cooperation of visa posts where your education and experience credentials are from - this task verifies your claims and authenticity of documents.
Security check is done by Canadian intelligence and security agencies, with or without cooperation of proper authorities in countries you lived/stayed in, and it is done completely independently from CIC - CIC only gets result, which will be positive or negative, without any explanation (as it is classified). This task looks deep into your life, activities and associations to find out if you are/were involved or are/were associated in any way with anyone who is/was involved in espionage, terrorism, organized crime, radical movements, crimes against humanity, war crimes, etc..
Criminal check looks into your police certificates and verifies with relevant countries to see if you have a criminal record that may make you inadmissible to Canada
