Nope, you're not missing a thing. I uploaded the wrong version of my script. Here's the portion you're questioning from the actual script:

while ($inLine = <IN>) {
        my ($ip1, $port1, $ip2, $port2) = 0;
        my ($date, $log, $protocol, $firstIP, $secondIP, $packets) =
                split(/,/, $inLine);
        # strip port number if it exists
        if ($firstIP =~ /([\d.]+)\((\d+)\)/) {
            $ip1 = $1;
            $port1 = $2;
        } else {
            $ip1 = $firstIP;
            $port1 = " ";
        }
        if ($secondIP =~ /([\d.]+)\((\d+)\)/) {
            $ip2 = $1;
            $port2 = $2;
        } else {
            $ip2 = $secondIP;
            $port2 = " ";
        }
[download]

After a quick review, that seems to be the only difference. Sorry for the confusion.

If things get any worse, I'll have to ask you to stop helping me.