Messages sent via Apple Mail are saved in "Sent Messages" folder rather than the "Sent" folder.
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Apple Mail defaults to a sent mailbox/folder named "Sent Messages". If the option to "Store sent messages on the server" is active it will create a folder called "Sent Messages" on the server and use that folder to save copies of sent messages. This conflicts with many other applications with use the folder "Sent" instead.
To change the default sent mailbox for Apple Mail first select the "Sent" folder on the server (in the folders pane on the left). Then chose Mailbox from the menu > Use this Mailbox for > and then chose Sent.