This is simply a file permissions error. The user you are connecting to with cyberduck does not have permission to perform file operations.
It is a good idea to try a similar SCP operation on the command line to double check that cyberduck is not playing tricks on you. Here you will see a quick "permission denied" error.
Make sure you connect as www data if the user who owns the file ... although it may be unusual to connect to this user. Alternatives? Log in as root. Try writing files to a different destination directory, for example. your user home directory or / tmp. This may be an adequate workaround if you can move the files after they are transferred, but in any case run this test as a health check.
Personally, I got into this error with one specific file, because I accidentally ran root to become the owner of the file itself (and not the directory in which it was), but your -R commands should take care of this.
Another piece of information I remember hit a bit: do you have SELinux?
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