Apple mail not separating emails into correct inbox

I have quite a few accounts setup in the apple mail app on my iMac. I am running version 10.9.5, when I receive new emails they are all going into one accounts inbox, it is not separating into the correct inbox for each individual account. I have checked and all preferences look fine.

Hi, is this a POP or IMAP acount?
Not certain, but this can fix myriad Mail problems...
Safe Boot from the HD, (holding Shift key down at bootup),  it will try to repair your Disk Directory while the spinning radian is happening, so let it go, run Disk Utility in Applications>Utilities, then highlight your drive, click on Repair Permissions.
Reboot, then in Mail, highlight that Mailbox, then in Mail's Mailbox menu, choose Rebuild... any change?

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