Found a great series of steps from the devloper on how to resolve issues:
Go into your phone settings, accessibility and switch off light flow
Then go into your phone settings, security, notification access and switch on lightflow
Go into your phone settings->application manager->select light flow and make sure "show notifications" is checked.
Then restart your phone (ie power it off and back on)
Go into your phone settings, display, led indicators and make sure only "notifications" is checked.
Go into lightflow, settings and make sure all of the following are off (they should be by default):
Samsung root mode
USA/Canada S3 mode.
Then go into lightflow, notifications, missed call and select the color red.
Press the phones "home" key and switch off the screen.
Then try get a missed call and see if the led flashes red.
If that works, then settings other notifications on should generally work.