This problem could occur if you have more then one version of the same application installed at the same time (you allowed side by side installs) or you have created projects starting from an existing one. In this case all the components share the same GUIDs and when one package in uninstalled the components referenced by the other applications are not removed.
In order to remove those files you have to uninstall all the packages that refere those components.
This problem had been eliminated in the 3.6 version of Advanced Installer. New GUIDs are generated when the version is changed.