Outlook 2013 Messages still going to Junk E-mail Folder even when Junk filter is turned off

The resolution for this was to login as the user via Outlook Web Access and disable it in there. To do this, log into OWA and go to Options > Block or Allow Settings and choose to turn it off – then save the settings.

There is a powershell cmdlet to disable this for Exchange 2010, Exchange 2013 and Office 365. The Cmdlet is

Set-MailboxJunkEmailConfiguration

You can find more info here: http://technet.microsoft.com/en-GB/library/dd979780(v=exchg.150).aspx