This is most likely due to Spam Assassin's Spam Box feature.
Spam Box is a feature for those using Web Mail and should only be turn on if you use Web Mail.
As time goes by the box is filled with Spam Emails and to correct this one has to login to Cpanel and click on Spam Assassin.
Once there click on the button Clear Spam Box which will remove all Spam messages from all your email accounts.
That should solve the problem but keep in mind you need to do this every so often as the spam can build up quite a bit.
Maybe in a future release they will have a auto setting for this that clears it every day for messages older than X number of days where you can set that number.
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