I am experiencing an issue with page numbering when compiling an Rnw file using different versions of LaTeX. Here’s a summary of the problem:

Older LaTeX Version (MiKTeX-pdfTeX 2.9.6499):

• First page: No page number.
• Second page: Page number 2.
• Last page: Page 18 (landscape orientation).

Newer LaTeX Version (MiKTeX-pdfTeX 4.1):

• First page: No page number
• Second page: No page number
• Third page: Page number 2
• Last page: Page 18 (It is empty and in portrait orientation, whereas all pages should be in landscape orientation.)

It seems that in the newer version, the first page is considered a cover page and is not taken into account in the page numbering, resulting in discrepancies with the expected page numbering sequence.

I suspect the problem is also related to the {everypage} package, which is now in legacy status.

I aim to achieve consistent page numbering behavior across different LaTeX versions. Ideally, I want the output to match the behavior of the older LaTeX version.

Below is a simplified version of my Rnw file:

documentclass[a4paper]{article}
usepackage{fontspec}
usepackage{pdfpages}
usepackage{hyperref}
usepackage{lastpage}
usepackage[paperwidth=8.27in, paperheight=11.69in, left=0.5in, right=0.5in, top=0.72in, bottom=0.75cm, includefoot, heightrounded, footskip=0.2in]{geometry}
usepackage[absolute,overlay]{textpos}
usepackage{pdflscape}
usepackage{everypage}

setmainfont[Scale=0.878]{Segoe UI}

definecolor{iblue}{RGB}{43,72,148}

% Define the position of the page number in the right margin
newcommand{rightpagenumber}{
  begin{textblock*}{1in}[1,0](paperwidth+0.65in,5.55in)
    rotatebox{90}{bfseries color{iblue} thepage of pageref{LastPage}}
  end{textblock*}
}

% Add the page number to every page except the first one
newcounter{pagecount}
AddEverypageHook{
  stepcounter{pagecount}
  ifnumvalue{pagecount}>1
    rightpagenumber
  fi
}

begin{document}

includepdf[pages=-, landscape, pagecommand={thispagestyle{empty}hypertarget{page.thepage}{}}]{report_1.pdf}
includepdf[pages=-, landscape, pagecommand={thispagestyle{empty}hypertarget{page.thepage}{}}]{report_2.pdf}
includepdf[pages=-, landscape, pagecommand={thispagestyle{empty}hypertarget{page.thepage}{}}]{report_3.pdf}

end{document}

All imported PDF documents are copies of the document created using this code:

documentclass[a4paper]{article}
usepackage{fontspec}
usepackage{lipsum}
usepackage[paperwidth=8.27in, paperheight=11.69in, left=0.5in, right=0.5in, top=0.72in, bottom=0.75cm, includefoot, heightrounded, footskip=0.2in]{geometry}
usepackage{fancyhdr}
usepackage{pdflscape} 

setmainfont[Scale=0.878]{Segoe UI}

% Configure fancyhdr to clear the default footer
pagestyle{fancy}
fancyhf{} % Clear all header and footer fields
renewcommandheadrulewidth{0pt}
renewcommandfootrulewidth{0pt}

% Custom command to insert Lorem Ipsum paragraphs with blank lines in between
newcommand{lipsumwithpar}[2]{%
  foreach i in {#1,...,#2} {%
    lipsum[i]vspace{1baselineskip}
  }%
}

usepackage{pgffor}

begin{document}

begin{landscape}

lipsumwithpar{1}{57} 
end{landscape}

end{document}