Track down some 0-byte files in the xferlog, see who the uploader was and/or track the source IP address by relaxing the hide-ip settings to show part of the ip address instead of hiding the whole thing (if you have that enabled) . You can then see if there is a pattern such that all the 0-byte files come from one sender or one site and then see if you can figure out what makes it special...
I seem to remember way way back the number one reason for some 0-byte files was the sender didn't have enough credits LOL.
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