Ok so I am trying to make a darker dungeon mod but some areas won't stay dark, helgen for instance when I move from one Room to the next the darkness will fade away to brightness, what am I missing, why won't the map stay at the darkness I have set, not all maps do this so its a bit annoying.

Do the rooms have different room bounds? Maybe the room bounds have different templates which are overriding your general cell settings? You can edit the lighting template of each individual room bound by clicking on the room bound and editing it's properties.