that the problem you have is that the pdf page numbers are not the same as the numbers on the page...
For example, often a pdf will be an exact copy of a printed document... the printed document may will have a cover, probably a blank inside cover, and then the first page of text will be "page 1"...
when this becomes a pdf, as far as the pdf is concerned, the cover is page 1, the (blank), inside cover is page 2, and the fist page of text, (which may actually have "1" printed at the bottom of the page), is, in pdf terms, page 3.
When you print and specify page numbers you have to specify the PDF page number, not the DOCUMENT page number. It's just a matter of shifting the page number up a few, (usually 2).
I don't know a way of doing this automatically... but it's not too taxing!
With apologies if this doesn't work, or I've got the wrong end of the stick!