I've moved your question from InDesign to the Acrobat Crfeating Editing and Exporting PDFs forum which is, I hope, someplace you may get more help since this is really a PDF problem.
No. Obviously this is not a PDF problem, but InDesign. As I have mentioned, InDesign creates PDF with and without "R/Type/Catalog/PageLabels"when folio beging with 1 and other than 1 respectively.
We expect, InDesign to create PDF with PageLabels irrespective of any folio it begins.
1. It sounds as if you are searching the PDF file as text, because of your reference to R. You need to use a PDF library to extract information as it may not be in useful text order, or may be in compressed streams.
2. Perhaps InDesign is not creating labels when they would have no effect; in this case it would be easy enough to default to page's actual numbers.
I still think you will get more help here than over in InDesign. Our users really don't know about the inner workings of the PDF library and what happens during export.
IF you don't get any help here after a reasonable time try agin ofer in ID and I won't move the new post, but don't hold your breath waiting for a response if you do.