Actually, delete duplicates was meant for when a user adds a POP account, downloads their mail, deletes that POP account, readds that POP account and redownloads their mail. If a user did that, they would end up with two copies of the mail in their POP account (assuming they had, leave mail on server enabled). This is probably a pretty rare occurance, so I've been thinking about removing the button since it's not too useful. It does work though, just that the emails have to be exact duplicates of each other (same headers as well).
Adrian