You said "Criminality clearance is valid for 1 year. Security clearance is valid for 4 years." but in the new tracker, there is only "Background verification" and "Prohibitions".Criminality clearance is valid for 1 year. Security clearance is valid for 4 years. Here's the source. Look under the "Clearances" section towards the bottom of the page.
What might have happened here is that CSIS might have had to initiate deeper checks for some reason. May be there was someone who was a person of interest or in a wanted list with a name/DOB/appearance similar to yours or you were a victim of some "random deep security checks". Security checks are done by CSIS (CBSA also shares some responsibility here as they investigate and clear you of crimes like crimes against humanity, war crimes etc).
Or it might be that they, for some reason, are looking much deeper into your physical presence as a temporary and a permanent resident. Can't be sure.
What is the current status of your criminality? Were you ever asked to submit fingerprints? Criminality clearance expires in 1 year. Criminality clearance is provided by RCMP.
Your case is taking very long. Try ordering GCMS notes from both CBSA and CSIS. Be very specific in your request - Say something like "Please provide all relevant information including the electronic notes of the officers pertaining to my citizenship application".
I'm surprised you haven't tried this already. I'm not sure whether this will speed up the application or not but you might at least get to know *something* about what's going on with that application of yours.
Do you know which one is which? Thanks!