I played around a little bit: by changing forcing secondary_win to generate the phwin (your !Exists block) and by making $mw process one event, I was able to make the main window draw first and end up first in my Win7 application bar...

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

use Tk;
use Tk::Pane;

my $mw = new MainWindow ();
$mw->title(" $0 MAIN");
my $phwin; # deleted '= $mw->Toplevel();': force it to be created by s
+econdary_win() function

my $fr0 = $mw->Frame(-borderwidth => 2, -relief => 'groove'
      )->pack();
    $fr0->Label(-text => "MAIN $0 MAIN"
      )->pack();

$mw->DoOneEvent();  # appears to force mw to draw itself _before_ seco
+ndary_win() creates phwin
sleep(1);           # makes it obvious that there's a delay; don't use
+ in production
&secondary_win;
MainLoop;

######################################################################
+##########
sub secondary_win {
    # window does not exists
    if (! Exists($phwin)) {
      $phwin = $mw->Toplevel();
      $phwin->title("SECONDARY");
    }
    # window Exists
    else {
      $phwin->deiconify( ) if $phwin->state() eq 'iconic';
      $phwin->raise( ) if $phwin->state() eq 'withdrawn';
    }
    my $scrolledframe = $phwin->Scrolled('Frame',-scrollbars => 'osoe'
+)->pack();

    my $sec_label = $scrolledframe->Label(-text=>'SECONDARY')->pack;
}
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