The problem is messageBox is a special kind of window that grabs the screen. If you make it a transient, as shown below, it works, but some Tk errors will get printed as you destroy the mainwindow, because the messagBox still has a screen grab. If the below changes are not workable for you because of the Tk dump of destroy errors, then consider using a plain toplevel window instead of a messageBox. 
my $status = $mw -> messageBox(
      -message=>"Do u want to start the process..?",
      -type=>'yesno',);
     
     if($status eq "Yes")     {
         $choice = "Yes";
         print "$choice\n";
         exit;
       }else{
        $choice = "No";
       }
    }
) -> pack(-side =>'right',-expand => 0); 

$status->transient($mw);  # will work, but causes harmless errors repo
+rted

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In reply to Re^4: Perl Tk exit the main window after 5 seconds... by zentara
in thread Perl Tk exit the main window after 5 seconds... by Anonymous Monk

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