It could be happening for any number of reasons. If his diet is adequate and he is getting enough amino acids, protein, vitamins, minerals and fat ect. Try washing his mane with a dandruff shampoo and see if it helps. Is he scratching his mane or acting itchy at all? Maybe the shampoo and conditioner are just drying that area out to much, try combing the flakes out and just leaving the area alone, and condition away from the roots. Give his natural body oils a chance to fix it.
My daughters horse was having the same problem she primped and combed and washed her pony daily. She was drying her out by removing the natural oils from her skin. Once she stopped the washing and went to currying and combing the flakes went away. Hope this helps.