Sorry if I've got the wrong end of the stick here, but NPM/NTA won't configure netflow on the router. You need to add this to the router's configuration manually prior to selecting interfaces for monitoring.
You're only selecting the interfaces you want to receive netflow stats for in NTA, you're not affecting any configuration changes on the router itself.
Make sure the interfaces you want to monitor have ip flow ingress stated in the configuration in addition to all the other flow-export commands.
NCM is the only platform that can be used to deploy configuration changes.