It was mainly for SMS, as that is the most common alert I receive. At first it works fine -- I receive an SMS, the light blinks at my set rate in the color I chose, I unlock the phone and go into the stock messages app and its own notification disappears as I read the SMS. I then lock the phone and the LED stays off.
It continues working that way for a while. Then after some time has passed, I receive an SMS and follow the same steps as above and when locking the phone after reading the text, the LED continues to flash. The stock messages app's notification has cleared itself, but the LED still blinks when the phone is locked. The only way to make it stop is to go into Light Flow and disable the app.
This happens both when plugged in and not plugged in. Makes no difference.
My phone is rooted, but this happens whether the root functionality in the app is checked or unchecked.
I haven't tried the manual option because I don't want to have the extra step of pulling down the curtain and clicking Clear every time.