Fur color fading, fur thinning and eyeliner light

Our dear little girl is now 17 months old. We rescued her 9 months ago from an abusive and neglectful "home". She was mostly in a crate, completely covered in urine and feces. The only way she managed to stay alive was to eat everything and anything available when she was released from her prison.

When she came to us, it took about 4 months to crate train her (we are still working on the housebreaking - getting better, but LONG way to go STILL). While she still tries to see what is interesting in the trash, try to 'raid' the litter box and steal any food not nailed down, she is almost 'normal' about it (no longer an absolute frenzy and single goal at all costs).

From the care, grooming, and exercise she received in our care, her brown nose became jet black, her eyes began to shine, her eyeliner became visible, and her coat became soft and very rich in color. In the last couple of months, she has begun to loose the color of her eyeliner and the color of coat is fading and her coat seems to be thinning.

Her last vet check (about 2 1/2 months ago) was perfect.

We are feeding her Purina Little Bites (at vet's suggestion, since he thought other brands might be too rich [both for dog's system and my poor budget]).

Any suggestions?