This is just a shot in the dark, but does your download tracking pepper utilize a unique URL to track downloads? For example, my past experience with the Downloads Pepper is that it requires URLs to be in this form:
yourdomain.com/mint/pepper/orderedlist/downloads/download.php?file=http%3A//yourdomain.com/yourfile.zip
While you can do your best to have this URL on your downloads page and share it with other interested parties, that means that Mint will not be able to count anyone who directly accesses yourdomain.com/yourfile.zip
I think the problem that you’re encountering, if I’m right of course, is that your server logs see both yourdomain.com/mint/pepper/orderedlist/downloads/download.php?file=http%3A//yourdomain.com/yourfile.zip and yourdomain.com/yourfile.zip as access to the same file, but the downloads pepper can only counting people who access the special URL.