WP-Filebase has a problem with query-strings attached to a files permalink. These can occur when e.g. MailChimp (http://www.mailchimp.com) automatically adds Google Analytics tracking data (campaign name and so on) to all links within a newsletter. The resulting link to a PDF ends up as:
Which results in a 404 because WP-Filebase uses $_SERVER['REQUEST_URI'] instead of $_SERVER['SCRIPT_URL'] when building the file path from the request. Changing occurrences of $_SERVER['REQUEST_URI'] to $_SERVER['SCRIPT_URL'] in classes/Download.php (function ShouldSendDLHeader()) and classes/Core.php (function DownloadRedirect()) fixes this behaviour.