No I was a PR throughout my 5 years. The only odd aspects of my application that come to mind are the following: my lack of presence in approximately the first 2 years & a gap in between the issuance of my passports.PR card is not needed I suppose since they have the UCI no and all the info.
Did you and @BOYX have temporary residence status as student/worker before PR? I am just wondering the reasons why it does not work for you guys.
And one more thing I noticed different in online application, though not related to issue you face. The online app does not ask for section 9b questions that are in the previous paper form [Form CIT 0002]. These questions are about the work/study permit history. For my case, i had these permits and only place to add was in the physical presence calculator form.