There certainly is no difference between the message's on MailBox's side. All messages are treated equal (and none is more equal than the other)

You may add some print statements to Mail::Transport::POP3 sub send() to trace the communication.

Or try a different POP3 client (mozilla?) to list the messages: do other POP3 implementations show the correct result? This to see on which side (client or server) the bug is.