When changing the settings of the running service configuration there is no effect on the running instances. This is because in the actual build, the service configuration changes are not being handled (RoleEnvironment.Changing event).
 
Workaround: reimage the running instances with the new service configuration file. If you have RDP enabled, you can also modify the bindings through the IIS management console to the running instances (the new ones will take the configuration from the service configuration file).
 
This will be fixed in a future release.