I've read in many, many places that it is often due to food allergies or intolerances and I have found a correlation empirically as well. When I've eaten a verboten food, one of the first indicators is that I'll have dark circles under my eyes which can even look reddish/purplish when it's quite bad. It's generally accompanied by pinkness and angioedema around the eyes, making me look tired even when well-rested.
"Paleo" diets eliminate a lot of common allergens, such as peanuts, gluten, and sometimes dairy, etc. But plants are full of other toxins and many "paleo"-approved foods are quite allergenic/sensitizing. My dark circles only really go away if I'm eating a strict 5-10 or so foods, such as chicken, tallow, green beans, beef, eggs, cashews, rice. It's quite difficult to stick to so I'm generally somewhat dark-circled. However, the dark circles actually largely disappear when I am truly strict with my diet. Just my two cents.