I don't know if your modifications might have affected this, but with a stock installation of OJS 2.1.1, this would indicate to me that your magic.mime database is probably old or incompatible with your installation of PHP. Have a look at http://www.php.net/manual/en/function.mime-content-type.php
for information on the function OJS uses to determine file types; if your PHP install doesn't support this function (you can check by calling function_exists('mime_content_type') and checking the return value), OJS works around it by executing the UNIX standard "file" tool via command line.
I don't know what would cause PDF images to stop working; I suppose it might be possible to have created your PDFs without embedding the images themselves...?
Rewrite rules or modifications might've caused #4; you'll have to investigate a little further. We haven't had problems like this with OJS 2.1.1.
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