It looks like OJS thought the PDF files were actually HTML. OJS detects file types using the mime_content_type function; if you search this forum for "mime_content_type" you'll find numerous posts on the subject. I'd suggest using a test script on your server to make sure types are being detected properly; something like:
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<?php echo 'Mime type: ' . mime_content_type('pdf_file.pdf') . "<br/>\n"; ?>
If you place this script on your server and a test PDF called pdf_file.pdf in the same directory, you should be able to call it in order to display the file type.
Alternately, if you imported using HTML files and later re-uploaded PDFs over top of the HTML galleys, that could be the cause of the problem. OJS only detects file types when the file is first uploaded.
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