Since I've moved away from "commercially manufactured juices", and mix my own (DIY), I've not had any issues with stains on my teeth (or in my tanks). The flavorings I use do not contain food-colorings or additives. I think @Jeffb is right... you're experiencing staining due to food color added to the juice to give it a pleasing color in the bottle.
Many companies do this... Chocolate should be brown... Strawberry should be red... Blueberry should be blue... when in reality, very few flavorings are the color you expect, and most of them are, in reality, clear or slightly tinted.