I also have a "red flag" in my passport because I was refused entry to Canada some years ago. I was trying to visit my husband and the officer did not feel I had sufficient ties to my home country. Any time I would go through the border again, I was automatically referred to secondary. I haven't yet crossed back and forth as a PR (still waiting on landing), but I hope it won't be too big of a deal then.
Are you guys referred to secondary inspection every time you enter Canada, even though he's now a PR? I can't see how his denied work permit would be relevant now, since they would only really care about that if he was coming as a visitor? I hope I won't be referred to secondary every time I enter Canada because of a "lack of ties" some years ago. My lack of ties back then is entirely irrelevant once I'll be traveling as a PR!