When you click a button on the window generated by messageBox(), the popup is destroyed. Any output you subsequently generate (e.g. from your system() calls) cannot be added to the popup text because the popup no longer exists.

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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