This works, just remove 'all' from your bind, as suggested above. Also, Scrolled Frames are not recommended, use a Scrolled Pane.

#!/usr/bin/perl
use Tk;
use Tk::BrowseEntry;
use Tk::Pane;
use strict;

my ($mw,$topframe,$font,$row,$i,$who);

my (@frame,@list,@label);

my (%var);

$mw = MainWindow->new();
$mw->geometry('1000x300+400+40');
$mw->title("Test GUI");
$mw->bind('<KeyPress-Return>', sub{shift->focusNext});

$topframe = $mw->Scrolled('Pane', -scrollbars => 'e',-height => 1000)-
+>pack();
#$mw->bind('all','<4>',=>sub{$topframe->yview('scroll',3,'units')});
#$mw->bind('all','<5>',=>sub{$topframe->yview('scroll',3,'units')});

$mw->bind('<4>',=>sub{$topframe->yview('scroll',3,'units')});
$mw->bind('<5>',=>sub{$topframe->yview('scroll',3,'units')});


$font = "-adobe-times-bold-r-normal--20-100-75-75-p-p-56-iso8859-1";
$row = 1;

for ($i =0; $i < 100; $i++) {
        $frame[$i] = $topframe->Frame(-borderwidth => '1', -relief => 
+'groove');
        $list[$i] = $frame[$i]->BrowseEntry(-variable => \$var{$i},
                        -takefocus => 0,
                        -foreground => 'black',
                        -disabledforeground => 'black',
                        -highlightcolor => 'green',
                        -font    => $font,
                        -width => 50,
                        -state => 'readonly') ->pack(-side => "left", 
+-padx => "5");
        $label[$i] = $frame[$i]->Label(-text     => $i,
                        -anchor  => 'w',
                        -takefocus => 0,
                        -foreground => 'black',
                        -font    => $font,
                        -width   => 50,
                        -height  => 1) ->pack(-side => "right", -padx 
+=> 5);
        $frame[$i]->grid(-row => ++$row, -column => 1, -sticky => 'e',
+ -padx => 5);
        $list[$i]->insert('end', (1..100));
}

MainLoop();
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