I have done more experimenting on this issue. I am using a MacBook Pro running CyberDuck 7.0.0.
In multiple cases, the files downloaded by Cyberduck do not match the original files. The size is different. I have tested the same files with FileZilla and the downloaded file is exactly the same including the same MD5.
Is this a problem I can fix somehow? I have turned off segmented downloads, however "open multiple connections" is active. I will try turning that off next and send a follow up.
Is it a binary/ascii issue? These are all binary (Video source content) files.