Protected pdf

Is there a reason why protected PDF files do not show in downloads? We have several of these in our website and they should be in the stats.
Normal (unprotected) pdf files can be found in stats.

Do the files have a standard *.pdf url? If the PDF are generate by a web application they may sometime have a URL like getDocument.php?id=closingcost. A url like would need to be explicitly marked for Download tracking.