I don't know what technique you are using to keep your window on top. But a more foolproof way, is to set a timer, that raises your chosen window every 10 ms (or so). This may not work, if your window manager settings are "focus follow mouse" or some similar setting.

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

my $top = new MainWindow;

keep_on_top($top);

MainLoop;

sub keep_on_top {
    my $w = shift;
    
    my $toprepeater = $w->repeat(10,
      sub{ 
              $w->deiconify;           
              $w->raise; 
   });

}
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