Sebastian,
Mail Eater configuration (Mailbox) in SDM 14.1 would be in Administration tab if you logon as SDM Administrator.
On the left pane, under Email >Mailboxes. Open the mailbox detail page from the Mailbox List.
There is Attachment Repository. The value 'Attach Entire Email' would affect how the email message handle with the repository.
The Attachment Repository also defines from Attachment Library >Repositories in Administration tab. You can find whether the EML Repository appears in one of Repositories.