Without seeing your code, it's difficult to make meaningful comment. Are you checking the return status of $server->delete($message_number) to confirm that your delete action succeeds? What does your expunge_mailbox return?

Updated:

Well, it looks like the module does not work as documented. The loop which generates the return code is:

    while ( $res = $sock->getline ) {
        my $ok = $self->_cmd_ok($res);
        if ( $ok == 1 ) {
            return $args{final}->($res);
        } elsif ( defined($ok) && ! $ok ) {
            return;
        } else {
            $args{process}->($res);
        }
    }
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Which plainly can return undef (counter to the docs). You could probably stick some code in there to print out the actual result. So the answer to your original question is, "Broken module"