I also get this problem, and have for the past few weeks. I sent you a private reply above with access to my site; additionally, it looks like Chrome throws a ERR_CONTENT_MISMATCH error, while Firefox and IE just download empty files (with the wrong name). My guess is that, as WP Download manager is opening up the zip files to get the individual ones, it is improperly constructing the HTTP headers (or perhaps not decrypting properly).
