There are two possible fixes for IMAP accounts. The first, and preferred, method is to add Inbox to the IMAP root.

Set a Root Folder

To do this, go to File, Account Settings and double click on your affected IMAP account. Click More Settings button then switch to the Advanced tab.

In the Root folder path field type Inbox. Exit the dialog and perform a send and receive. (If the Inbox is not your root folder, setting Inbox as the root won't work, as it will hide all of the other folders.)

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