Thank you for your question. I looked into this further and noticed cyberduck had an issue regarding this that was corrected in a later release. So, I first recommend making sure you are using the latest version of cyberduck.
I would also recommend checking the permissions of the parent folder you are uploading to, as it may be inheriting permissions from parent folder.
In case you need it, here is a link to our article on how to change permissions from cPanel.
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