Ok, here is a simplified version of the program. All it has is a right click menu and a left click interface. The procedure is still the same you have to select VCI from the menu first. The window shows but I cant get it to hide when the user left clicks the system tray. I tried to print the $visible variable and it does not seem to change from 0.

#!/usr/bin/perl -w
use strict;
use warnings;
use Glib qw/TRUE FALSE/;
use Gtk2 '-init';
use Gtk2::TrayIcon;

#global variables
my $current_controls = 0;
my $visible = 0;

#icon goes in box, box goes in tray
my $icon = Gtk2::Image->new_from_stock(  'gtk-open', 'menu');
my $eventbox = Gtk2::EventBox->new;
$eventbox->add($icon);
my $tray = Gtk2::TrayIcon->new('Test');
$tray->add($eventbox);

#events and timeouts
$eventbox->signal_connect('button_release_event', \&click);

#show tray
$tray->show_all;

#end event loop
Gtk2->main;


#handles tray clicks
sub click {

    #left mouse button
    if ($_[1]->button == 1) {
        
        #Window show/hide controls
        if ( $current_controls != 0) {
            if ( $visible == 0) { $visible = 1 }
            if ( $visible == 1) { $visible = 0 }
                        &interface;
        }
        
    }
    
    #right mouse button
    elsif ($_[1]->button == 3) {
        &menu;
    }
    return 1;
}


#right click menu 
sub menu {
    my $menu = Gtk2::Menu->new();

    #VCI
    my $menu_VCI = Gtk2::ImageMenuItem->new_with_label("VCI");
    $menu_VCI->signal_connect(activate => sub { $current_controls = 1}
+);
    $menu_VCI->set_image(Gtk2::Image->new_from_stock('gtk-refresh', 'm
+enu'));
    $menu->add($menu_VCI);

    #configure
    my $menu_pref = Gtk2::ImageMenuItem->new_with_label("Configure");
    $menu_pref->set_image(Gtk2::Image->new_from_stock('gtk-preferences
+', 'menu'));
    $menu->add($menu_pref);

    #separator
    my $menu_sep = Gtk2::SeparatorMenuItem->new();
    $menu->add($menu_sep);

    #Quit
    my $menu_quit = Gtk2::ImageMenuItem->new_with_label("Quit");
    $menu_quit->signal_connect(activate => sub { Gtk2->main_quit});
    $menu_quit->set_image(Gtk2::Image->new_from_stock('gtk-quit', 'men
+u'));
    $menu->add($menu_quit);
    
    
    $menu->show_all;

    #popup menu, the three is for right mouse button
    $menu->popup(undef,undef,undef,3,undef,undef);

    return 1;
}

#Program interfaces
sub interface {
    my $interface = Gtk2::Window->new('popup');
    $interface->set_position('center');
    
    #Eventbox for capturing the mouse click
    my $eventbox_interface = Gtk2::EventBox->new;
    
    #table to contain the widgets
    my $table_interface = Gtk2::Table->new( 8, 2, FALSE);
    
    #menu items for VCI
    if ( $current_controls == 1) {
        
        #Labels
        my $label_vci_downloading = Gtk2::Label->new( 'Downloading');
        my $label_vci_uploading = Gtk2::Label->new( 'Uploading');
        
        #Bold text for the Main Labels
        my $fontdescription = Gtk2::Pango::FontDescription->new;
        $fontdescription->set_weight( 'bold');
        $label_vci_uploading->modify_font( $fontdescription);
        $label_vci_downloading->modify_font( $fontdescription);
        
        #labels for the progressbars
        my $label_vci_uasposition = Gtk2::Label->new( 'uasposition');
        my $label_vci_waytemp1 = Gtk2::Label->new( 'waytemp');
        my $label_vci_waytemp2 = Gtk2::Label->new( 'waytemp');
        my $label_vci_wayfinal = Gtk2::Label->new( 'wayfinal');
        
        #Horizontal Separator
        my $hseparator_vci = Gtk2::HSeparator->new;
        
        #Connect button-> will switch to stop after press
        my $menu_vci_connect = Gtk2::Button->new("Connect");
        
        #Attach the widgets to the table 
        $table_interface->attach_defaults( $label_vci_uploading, 0, 2,
+ 0, 1);
        $table_interface->attach_defaults( $label_vci_uasposition, 0, 
+1, 1, 2);
        $table_interface->attach_defaults( $label_vci_waytemp1, 0, 1, 
+2, 3);
        $table_interface->attach_defaults( $label_vci_wayfinal, 0, 1, 
+3, 4);
        $table_interface->attach_defaults( $label_vci_downloading, 0, 
+2, 4, 5);
        $table_interface->attach_defaults( $label_vci_waytemp2, 0, 1, 
+5, 6);
        $table_interface->attach_defaults( $hseparator_vci, 0, 2, 6, 7
+);
        $table_interface->attach_defaults( $menu_vci_connect, 1, 2, 7,
+ 8);
        
        #button function
        $menu_vci_connect->signal_connect( 'button-press-event' => sub
+ { my $button_vci_label = $menu_vci_connect->get_label;
                                                        if ( $button_v
+ci_label eq 'Connect') {
                                                            $menu_vci_
+connect->set_label( 'Stop');
                                                        }
                                                        else {
                                                            $menu_vci_
+connect->set_label( 'Connect');
                                                        }
                                                    });
                                                }
    
    #add the widgets to the window: widgets->table->eventbox->window
    $eventbox_interface->add( $table_interface);
    $interface->add( $eventbox_interface);
    
    $interface->show_all;
    
#    if ( $visible == 0) {
#        $interface->hide_all;
#    }
#    else {
#        $interface->show_all
#    }
}
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