I had been stuffing around with different led apps to get it to do what I wanted. In the end I decided that things weren't how I wanted so I turned the led's off and removed all apps that managed the leds. They behaved like yours, flashing regardless of the setting being off. turning them on, then off made no difference.
In the end I just went back to lighflow with accessibility turned on - I had to remove any folders from my homescreens as the talkback kills me, but otherwise they do what I want and don't flash during the night.
But yeah, they ended up like yours and I couldn't stop it. I would guess a reset would fix it (I'm tired of reseting phones/tablets so didn't want to do that again)