In your case, it is difficult to say what is causing issues with linking. Technically if it is in the system, I don't see any reason why you cannot link it. I did it many times before for paper-based temp resident visa applications. Try every possible combination while linking.Yeah I did link my paper based PR though.
But PR Card one is not when I called to agent she said you may not link as its first PR card. But as per you my PR card application is still not in system?
What the agent is saying doesn't sound right looking at some posts in this forum.