So please, reduce this to a minimal script, which uses pre-defined icons instead of the pngs, get rid of the annoying balloons, and the sftp stuff. Show us a script that simply concentrates on the problem you describe, i.e. popping up a window when clicking on a trayicon.

I will be willing to bet, that in the process of simplifying this down to it's basics, you will find the glitch. But as it stands now, your script presents too many extraneous hurdles for us to casually spot your error.

But just as a quick push in the right direction, you need to bind the interface sub to a left click.

#events and timeouts
$eventbox->signal_connect('button_release_event', \&click);
# add a left click binding
$eventbox->signal_connect('button_press_event', \&click);

#handles tray clicks
sub click {

    #left mouse button
    if ($_[1]->button == 1) {
        
        #Window show/hide controls
        if ( $current_controls != 0) {
            #&interface;
            if ( $visible == 0) { $visible = 1 }
            
            if ( $visible == 1) { $visible = 0 }
        }
################################
# call the interface window if a left click is done
    &interface;
##############################

    }
    
    #right mouse button
    elsif ($_[1]->button == 3) {
        &menu;
    }
    return 1;
}
[download]

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
#    }
}
[download]