Programs like Foxit Reader and Adobe try to install toolbars, put shortcuts where you don't want them and links to third party web sites on your desktop, etc. Each time you run the update you have to manually uncheck all those options which are checked by default.
Another problem is that the programs that do update themselves do so by each running their check on Windows startup or own service ALL THE TIME.
A far better solution would be for Windows update to allow other programs to register for update checks that can then be handled by a single service.
