I believe that may be rather tricky with Runbox' webmail filters.
However, if you check your mail with a mail client, the client might support more complex filters like
Code:
If mail is from abc and recipient is foo then move mail to folder duplicates.
where
abc is the actual sender and
duplicates a folder to which you can copy the duplicate emails.
If you receive duplicate mails at foo@server and bar@server, this might be an approach.
Caution! Test the filter thoroughly to make sure you don't inadvertently delete any important mail. I'd highly recommend not to automatically delete any mails until you are 100% sure that the filter works exactly as you want it to work.