Yes I'm having trouble with after I get a message the light won't clear - you have to go in and close down the app to get it to turn off. I've never used LightFlow before as I'm coming from a Galaxy S2 that didn't have a notification light. Didn't know if I needed to use any special settings.
There are several ways to dismiss the LED indicator. Open Light Flow, choose Notification at top right. Under Notification, pick one of your apps. Again under Notification, there is a section called "Clear notification style" with 4 options:
1. Screen: when screen is switched on
2. App: notifying app entered
3. Reminder: when snoozed or cleared
4. Unlocked: when phone unlocked
That's where you choose when the LED clears and you'll have to do it for every app you've added to Light Flow. For instance, I have all my notifications set for unlocked, so the LED stops blinking once I unlock my phone.
If you need more help, there is a
discussion thread at XDA that has screenshots of the steps I've described above.