Mail shows same email

I've upgraded a Mavericks iMac to Yosemite and since then Mail shows the same email in each of the three different mailboxes.
I've tried to reinstall the Mac and I've also tried creating a local account but it's the same problem whatever account you log in to.
All accounts are IMAP and not even OS X 10.10.2 fixed this.
Are there anyone else out there who's got the same problem?

Try re-indexing the mailboxes. This can take awhile if you have a lot of mail.
Reindex messages      Mavericks/Yosemite

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