It is really confusing when Cyberduck successfully completes a sync then reports transfer incomplete. This is great software and I love it but that bit has thrown me for a loop. Can't it report that it successfully uploaded all changed files instead of reporting that the transfer was incomplete?
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I also see this same problem. The first time you sync a folder, Cyberduck reports "Transfer Complete". If you immediately do another sync on the same folders without making any changes, you get a "Transfer Incomplete" message.