Background check is just another step in the process that everyone of us goes through. It's not related wether they have doubts about a relationship or not. Two months is no unusual, there are many factors and agencies that affects the length of it.
The best is to contact them through a webform,(only if you have crossed the 12 month mark). Or try calling them and see what they can tell you about the status of your application. As well as ECAS and the CIC account.