Documents often use Roman numerals to number pages in the front matter, followed by Arabic page numbers (starting at 1) for the primary content. By default, PDFs label pages beginning with 1, ignoring restarts and so forth.
To change this behavior, forcing PDF page labeling to track the current (printed) page number, add the following request to your header processing:
.pdfmark /Label (\\n%) /PAGELABEL
If using -ms or -mspdf, this request can be added to the .HD macro. The only caveat is to make sure the page number format change (using the .af request) happens before the page break that starts page 1. In any case, the pdfmark macros must be included either by using -mspdf or explicitly including -mpdfmark in the groff command line arguments.