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This problem has been solved on my end. I’m not sure what exactly changed, but user error was probably one issue.
I am also having this problem. Just installed the app tonight and things went smoothly up to the point when I tried to manually stamp the pdf. I tried pdfs of different lengths, including single-page docs. I am using pair.com hosting, which is running PHP 5.2.13.
edit: also, I did go through the PDF creation checklist from the FAQ post. I created a single-page PDF saved from Illustrator and put it into the default stored-files directory.