First, it's not the "Synaptics add program thing"--it is the Synaptic Package Manager. It does much more than just add programs.
Please post the exact details of what you are doing. For example, if you click on a package you have multiple options, including install, remove, upgrade, etc. Once you select an option, then you would click "apply".
There's no "refresh"--only the "reload" button. This you use only if you have changed the repositories.