My pomegranate tree is 4 yrs old. Great fruit until this past year. The kernals are shaded from clear to darker pink. None of the fruit had dark red kernals when ripe. My mother, 1 mile away, has had the same problem for years, but her trees lack attention.
Pomegranate Tree Fruit
I have not heard of this happening. My initial reaction would be that it was weather changes or a change in radiation from the sun, but that would not explain why your mother's tree is like that. Did you get your seeds from her? It could be a genetic problem. Good Luck and Happy Growing!
Sorry, but I can't find an answer to your question. UC Davis has a pomegranate program. They may be able to give you the answer. Good luck.