Include and exclude files settings are not saved when using repository or work area changes from Windows shell extensions. When using deliver or update the include and exclude files fields are saved when clicking on next on the first screen. Any changes or additions made to the include/exclude files fields for work area changes or repository changes are not saved to the registry.
If you have multiple projects at the top level in an application then you cannot save the submit tree unless you make a change in the first one in the list.