I contacted Spellbinders with this problem and was told that many people are experiencing it.
The woman said try washing them in mild soap and scrubbing them with a "soft" tooth brush. She also suggested putting a piece of tissue paper between the die and the CS, but that didn't solve the problem for me.
She said after multiple uses the paint usually stops flaking off. She also said they are in discussions with a different manufacturer who claims they can solve this problem
I just use my finger nail on all of the cut edges to remove the paint flakes . It is a tedious task on dies such as Fleur de Lis