As kcott pointed out, the messagebox is not the right widget for displaying realtime output, it is meant for simple messages. Also, the messagebox destroys itself when you hit the Ok button, meaning that "you got the message".

Here is a simple way to do what you want. I substituted different commands for the iptables commands, because that requires root, or sudo. Anyways, I'm not altering my firewall rules to test your script. :-)

#!/usr/bin/perl
use warnings;
use strict;
use Tk;

# Main Window
my $mw = new MainWindow;
$mw->geometry('+100+100');

my $label = $mw -> Label(-text=>"Hello folks") -> pack();
my $button = $mw -> Button(-text => "Click here to Flush rules",
                -command =>\&flush) -> pack();
MainLoop;


sub flush {
$mw->messageBox(-message=>"Initiating flushing.. click on OK button");
# the script hangs here, until the messagebox OK button is pressed.

my $text = $mw->Scrolled('Text')->pack();

#my $out1 =  `iptables -L`;
my $out1 =  `ls -la`;
$text->insert('end',"$out1\n");
$text->see('end');

#my $out2 =  `iptables -F`;
my $out2 =  `dir`;
$text->insert('end',"$out2\n");
$text->see('end');

#my $out3 =  `iptables -L`;
my $out3 =  `ps auxww`;
$text->insert('end',"$out3\n");
$text->see('end');
}
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