We are having the same problem with our new puppy, we don't think it's the food because we kept her on the same food that the breeder was giving her. We had the same problem with our last Basenji every spring and fall. I suppose she may have been bitten without us knowing but we think there may be something else in the environment, either in the house or outside.
Do you have hot air vents on the floor? Did your last Basenji or present puppy have welts all over their body? Our puppy was extreme!! Her swollen eye disappeared when the body welts appeared. It was like a demon running through her body! The progression was very strange!!!