Well that would explain it if on some days you were only getting 3 calories! Kidding aside, it is interesting you were having problems when it looks like you were meeting your caloric needs.
Did you use an app like cronometer to help calculate? I've never been fully raw, but I'm vegan most days of the month and have done a couple of days out of the month totally raw and when I calculate on the days I'm totally vegan, the only nutrient that's kind of hard to meet is choline. Sometimes calcium, selenium, vit E, and zinc are not, or barely met, but then on other days they are well met so it would make up for days not met. I really only find choline the hardest to meet.
Any specific nutrients seemed to be lacking consistently on that diet for you?