Is it possible to be subconsciously afraid of the dark?

It sounds like you have adjusted your sleep schedule to where you are still able to go about your day, so it seems like you're doing alright for yourself. Perhaps you should see a doctor and find out the source of your nightmares, like if you are on any medications? For example, the nicotine patch, if worn over night, can cause nightmares. I knew a man who was taking a prescription tablet to cease smoking, it gave him frightening nightmares to where he stopped taking the medication and just started smoking again.