I had the same bad experience with Chaco liners. The yellow was the worst, but the gray/silver and the red were bad too. I used them to make flannel rag quilts for my grandsons and NONE of the lines came out and the quilts were ruined!
I pre-washed all of the fabrics AND I tried to brush it off before I washed the quilts. I was so disgusted...those markers aren't cheap, either! Threw them all away.
I now use the Crayola ultra-clean markers and have never had a problem with them - they always wash completely out, even after I've ironed over them.
I'm so sorry about your quilt - I know firsthand how discouraging it is.