I have recently added a WCF service reference to my program. When I perform a clean install of this program, everything seems to work as expected. But, when I install the program on a client which already has a previous version (without the new service reference) installed, I get a exception telling me the default endpoint for this particular service could not be found.

It seems that the appname.exe.config is not being updated with the new endpoint settings. Is there any reason for this and how can I force the installer to overwrite the config file? I'm using the default Visual Studio 2008 installer project with RemovePreviousVersions set to True.

Update: My program encrypts the settings section after the first run with the following code

Configuration config = ConfigurationManager.OpenExeConfiguration(ConfigurationUserLevel.None);
        ConfigurationSection section = config.GetSection(sectionKey);
        if (section != null)
        {
            if (!section.SectionInformation.IsProtected)
            {
                if (!section.ElementInformation.IsLocked)
                {
                    section.SectionInformation.ProtectSection("DataProtectionConfigurationProvider");
                    section.SectionInformation.ForceSave = true;
                    config.Save(ConfigurationSaveMode.Full);
                }
            }
        }

When I do not run the program before installing the new version the app.config gets updated.