Man, you seem to do everything so as to make it as hard as possible to figure out. :-)

Look at this code, with comments to show fixes.

#!/usr/bin/perl -w
use strict;
use Glib qw/TRUE FALSE/;
use Gtk2 -init;
use Goo::Canvas;

#variables
my $ellipsoid = 23; #static WSG83
my $zone;
my @mtp;
my @ps;
my @cs;
my $count = 1;

# changed to bring more into field of view
my $way_ref = [40, 70,140, 130];

#Create Window
my $window = new Gtk2::Window ( "toplevel" );
$window->signal_connect ("delete_event", sub { Gtk2->main_quit; });
$window->set_border_width (10);
$window->set_size_request(640,480);
$window->set_position('center');

#Create Scrolled Window
my $scwin = Gtk2::ScrolledWindow->new();
$scwin->set_policy('always','always');
$window->add($scwin);

#add canvas
my $canvas = Goo::Canvas->new();
$scwin->add($canvas);
my $root = $canvas->get_root_item();


# this group isn't doing anything, so when you add
# your PolyLines to it, it isn't there. You need to place
# the group somewhere on the canvas
#waypoint lines group
my $way_group = Goo::Canvas::Group->new($root);

#add Background image
my $filename = shift or die "no image $!\n";
my $pixbuf = Gtk2::Gdk::Pixbuf->new_from_file ($filename);
my $image = Goo::Canvas::Image->new($root, $pixbuf, 0, 0,
    'width' => $pixbuf->get_width, 
    'height' => $pixbuf->get_height);

#handle the events
$canvas->signal_connect (event => \&event_handler);


# your TRUE option below creates closed lines, you may want FALSE
#Start the waypoint connector, notice group is $root, NOT $way_group

my $way_lines = Goo::Canvas::Polyline->new($root,TRUE,undef,
    stroke_color => 'pink',  #make more visible
    line_width => 5,
    );

# PolyLine wants an Points object
my $points = Goo::Canvas::Points->new($way_ref);

# setting after line creation, sets the 'points' property by name
$way_lines->set(points => $points);


$window->show_all;

Gtk2->main;

#------------------------------------------------
#handle the mosue events
sub event_handler {
    my ( $widget, $event ) = @_;
    
    #on 2 mouse presses, a doubleclick
    if ( $event->type eq "2button-press" ) {
        my ($x,$y) = ($event->x,$event->y);
        print 'x->',$x,'  ','y->',$y;
        
        #Drop waypoint icon
        my $tgroup = Goo::Canvas::Group->new ($root);
        Goo::Canvas::Ellipse->new($tgroup,$x,$y,7.5,7.5,
            fill_color => 'purple',
            stroke_color => 'black');
        Goo::Canvas::Text->new ($tgroup,$count,$x,$y,-1,'GTK_ANCHOR_CE
+NTER',
            font => 'Sans Bold 15',
            fill_color => 'pink',
        );
        print " $count\n";
        
        push @$way_ref,$x,$y;
        my $points = Goo::Canvas::Points->new($way_ref);
        $way_lines->set(points => $points);
        $count++;
        print "$way_lines\n";
        return;
    }
}
#------------------------------------------------
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