I didn't know that there were POP3 email VIs. I see only SMPT VIs in my collection.
In your implementation, are you sure that you are connecting to the server, logging into it with the password, retrieving the mail, and trying to delete it without losing the connection?
There are only two possibilities. Either your session is being disconnected, or the delete command is not being received by the POP3 server. Check to make sure you aren't reconnecting before trying to delete. If that isn't the case, I would suggest either probing the output to verify the command is sent (I don't know what that command is, or even how to listen for it, other than to setup a relay server)) or contacting NI for additional support.
