again, what are your settings? IMAP, POP3, etc.
Also, is the email getting downloaded from your mail server a second time, or is it simply not staying in the trashcan (in workspaces panel)?
Next time it happens look in your trashcan to see if the deleted email is still there. If it IS still in there AND you have it in your inbox then that means that you got it a second time from the mail server.
If it's NOT in your trashcan and is in your inbox, then it's not staying trashed.
I don't know how to solve either of those problems off the top of my head, but maybe we can figure out exactly what the problem is.