Server deleted e-mail remaining on iPad

Hi all, I have an odd one for you.
I have pop3 e-mail accounts that I have setup on my iPad, but from my work PC I also use webmail.  I have sync'd the iPad to my mail account and all went well. When I delete e-mail on my iPad I have it set so it deletes the mails from the server and this works correctly. But when I delete e-mail using the webmail they remain on the iPad.
What have I set wrong?
I have a brand new iPad 4

Ok, here goes....
E-mail sent to my email address.
Log onto webmail and email is invisible.
Check for new email on iPad and email downloads
Check webmail again and email is still visible
Check iPad again and email is still there
Log back onto webmail and delete email
Check email again on iPad (inc. send & receive) and email is still visible on iPad
At this point on the android device the email would've been removed from the tablet

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