It has come to our attention that many Outlook 2013 and Office 365 users are having issues within synchronizing IMAP folders recently.This appears to be happening across all hosts due to a recent update that Microsoft has pushed out to all of its users.
However, it is now also more important than ever to correctly set the Root Folder Path for your mailbox when your IMAP server requires it.
Unfortunately, Outlook doesn’t detect this automatically but you need to set it manually.
I am running Outlook 2013, which I (sometimes) use to read my IMAP email.
However, I can see using the server-based mail reader (squirrelmail) that Outlook is not properly syncing my Inbox folder - Outlook thinks there are 89 messages, but there are really 91.
Visit your Account Settings, then Advanced for the mail account that you are having trouble with.