We are having a similar issues. Sometimes the files will upload to the server and sometimes they wont. We created all of our packages and then realized that when you click the download button for either the individual files or the full package, only some of them work. The download-manager-files folder seems to have 755 on it. Should it be 777? I’m assuming not. Why would some of the downloads work and some not? We checked inside of the directory and only a few of the files are making it all the way up, it’s not a file size issue either because some large files make it after a few tries and some small ones don’t make it up even though the package shows that it did. However, the files are missing from the directory on the server. Does this all make sense? We are using WP 3.5.1