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I believe Mac Mail uses Preview to view the PDF. Preview isn't the best for viewing PDF's.
You may want to ask your question in the Mac Preview forums.
so does my browser (safari) use preview as well? because when I click the link above and view the 10-page edition in my browser, the ad doesnt show up.
and doesn't it seem odd that it is able to be viewed in the original PDF file but not the PDF file I copied and pasted it into?
Yes. It does.
Acrobat 9 and older versions paste images as a stamp/comment which (that poorly functional) Preview cannot see, so you need to "flatten" the page if you want to see a pasted picture in Preview.
(Preview, Mail and QuickLook shares the same rendering library)
You can easily flatten one or several pages in a PDF using this free tools: http://abracadabrapdf.net/articles.php?lng=fr&pg=717