Just finished the call with IRCC agent like you did. My wait time was approx. 28 minutes. The agent was nice and friendly. My current status now is surprisingly similar to you: Eligibility - Not started, Security - Not started, Criminality - Passed, Visa Office - Ottawa.Just got off the phone with ircc agent. Wait time was 25 minutes. Surprisingly he was extremely helpful and polite. Below is the status of my application:
Eligibility - Not started, Security - Not started, Criminality - Passed, Visa Office - Ottawa.
The agent told me that, there are 2 documents which needs verification and because of them Eligibility and Security says "Not Started". Once those documents are verified, file would move faster. Nothing required from my side.
I have not paid RPRF. I will wait till (and if) they request for it.
After checking on the system, she said since my AOR, there has been no progress or updates on the system although it passed 6-month processing period. So she promised to send a reminder to the officer and try to put it on the priority. Hope that could help. Fingers crossed.