I worked out why it was doing it.
I found that if i had been having a text conversation and left the messaging screen open when the phone locked itself then the LED would blink. unlocking and going back into the messaging screen would stop it. Its as if it blinks because it doesnt know if you have actually read the text beacuse you were already on the screen
hands up if anyone understood any of that.
You can set it up within Light flow, how notifications should be cleared. I've mine set to "screen on".
On default I think its set to "App entered". So even if you clear the notification, it will still keeping blinking until your enter the app.