I think you should call the Save method
ConfigurationManager.Save(ConfigurationSaveMode.Modified);
ConfigurationManager.RefreshSection("appSettings");
EDIT
To be able to save you have to use a configuration object returned by the OpenExeConfiguration Method
//Create the object
Configuration config = ConfigurationManager.OpenExeConfiguration(ConfigurationUserLevel.None);
//make changes
config.AppSettings.Settings["Username"].Value = txtUsername.Text;
config.AppSettings.Settings["Password"].Value = txtPassword.Text;
//save to apply changes
config.Save(ConfigurationSaveMode.Modified);
ConfigurationManager.RefreshSection("appSettings");
More references here ConfigurationManager Class