If $run_all_button->flash() dosn't work, you can make one manually with a timer. See second script below. I'm guessing it flashes once, and so fast you miss it. You may need to add a timer.

As to your button states, look at this script.

#!/usr/bin/perl
use Tk;

$mw = MainWindow->new(-title => "Testing Stop Button\n");

my $toolbar = $mw->Frame->pack(-side => 'left');

$button_run = $toolbar->Button(-text => "RUN",
   -command => sub{
             $mw->Busy(-recurse => 1, -cursor => 'watch');
             $button_run->configure(-state => 'disabled');
             $button_stop->configure(-state => 'normal');})
       ->pack(-side => 'left');


$button_stop = $toolbar->Button(-text => "STOP",
   -command => sub{
        print "sub called, not Click_stop\n";
        $stop_spyglass = 1;
        $button_stop->configure(-state => 'disabled');},
            -state => 'disabled')
            ->pack(-side => 'left');

$button_stop->bind( '<Leave>', \&Leave_stop);
$button_stop->bind('<Enter>', \&Enter_stop);
$button_stop->bind('<Button-1>', \&Click_stop);

sub Enter_stop {
  print "Enter_stop ", $button_stop->cget('-state'), "\n";
    if ($button_stop->cget('-state') eq 'active' ){
      $mw->Unbusy();
    }
}

sub Leave_stop {
 print "Leave_stop ", $button_stop->cget('-state'), "\n";
   if ($button_stop->cget('-state') eq  'normal'){
     $mw->Busy(-recurse => -1, -cursor => 'watch');
   }
}

sub Click_stop{
  print "Click_stop ", $button_stop->cget('-state'), "\n";
   if ($button_stop->cget('-state') eq ('active')){
       $stop_spyglass = 1;
       $button_stop->configure(-state => 'disabled');
       $button_run->configure(-state => 'normal');
      }
}

MainLoop;
[download]

and a button flasher

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

my $mw = tkinit;

my $button = $mw->Button(-text => 'Push Me')->pack;

$button->configure(-command => [\&Invert, $button]);

my $button1 = $mw->Button(-text => 'Flashy')->pack;

my $timer = $mw->repeat(500,[\&Invert, $button1]);

MainLoop;


sub Invert {
my($w) = @_;
$w->configure(-bg => $w->cget('-fg'), -fg => $w->cget('-bg'));
}
[download]