Why does my merged PDF look wrong?

A merge copies pages. It does not “normalize” them. If the inputs disagree about paper size or rotation, the output disagrees too — on purpose. Viewers hide that. Printers do not.

Page size mismatches

US Letter is 612×792 pt (8.5×11 in). A4 is 595.28×841.89 pt (210×297 mm). Letter is 16.7 pt wider and 49.9 pt shorter. Merge a US offer letter with a European ID scan and you have two MediaBoxes in one file. On screen, each page is scaled to the window, so both look “full.” In print, “actual size” on Letter stock clips ~15 mm off the A4 page’s height. “Fit to page” scales the Letter page down and leaves a strip. Neither is a merge bug.

Fix it before you combine: reprint or rasterize the odd pages to the stock you will load, or pick one paper size in JPG to PDF if the source is photos. Then merge.

Orientation conflicts

Phone scanner apps often write a landscape MediaBox (792×612) plus /Rotate 90. Chrome applies the rotate and you see a portrait page. Some printers and some preview panes ignore /Rotate on merged files and spit out a sideways page. Check thumbnails in the merge list. If a page looks wrong there, it will look wrong in the download. Exclude it, re-export that scan upright, add it again.

Bookmarks and links after a merge

“Section 2” in file B pointed at page 4 of B. After B is appended to a 15-page A, that destination is still “page 4,” which is now in A. Internal links go to the wrong sheet. We do not rewrite outlines. If you need a table of contents, build it in the merged file.

Blank scanner sheets are not harmless: a white JPEG can be 2–4 MB. Expand the file in the merger and click the thumbnail to drop it.