This is only a workaround but as long as no better answer is available, this solves at least the current problem: It seems the "output" generated by the pax package (more precisely the JAR file within that package) contains computations that lead to an overflow in the TeX engine. The pax package tries to keep PDF annotations when including PDFs. Since in the current situation no annotations need to preserved, the workaround is to first extract the table using pdfpages to a separate PDF without annotations (say, table.pdf and the page of the original PDF with that table was 42). Then the main file can be changed as follows using the separate PDF instead of all pages of the original.
\documentclass{article}\usepackage{pdfpages}\usepackage{pax}\definecolor{linkcolor}{rgb}{0,0,.35}\usepackage{hyperref}\hypersetup{colorlinks=true,allcolors=linkcolor}\begin{document}\includepdf[fitpaper=true,pages=2-41]{04/sample.pdf}\includepdf[fitpaper=true]{04/table.pdf}\includepdf[fitpaper=true,pages=43-]{04/sample.pdf}\end{document}