How to figure out which app changes pulse notification light in system settings? The nexus 5 has this "pulse notification light" that blinks when the device is sleeping and you receive an email, sms or something like that. I don't like it, so I turned it off in Settings > Display by unchecking "pulse notification light" 

That works all fine for a couple of days/weeks but then suddenly the pulse notification light is back! And if I go to Settings / Display the checkbox is checked again! So one of my installed apps must enable this notification light again.

I want to figure out which app does that (most likely it is sms, mail or a chatting app). I guess notification light can only be enabled if the app has the System Settings permission, or is maybe the Vibrate permission enough? What is the best way to figure out which app actually made changes to my System? Is this logged somewhere?
You should check which is the first notification after your notification light is turned on automatically. Most probably that app is the one that is overwriting your permission, and as per my observation most of the apps that can access notification light have an built in option in their settings to disable led notification. You should try disabling it from there.