Did you heat set the markings, perhaps? I've found if I spray with water teh markings before pressing anything, they come out easier.
You might want try to a little lemon juice spritz on the marks you are having trouble with and hang it where the sun can get to it. I've had really wonderful results of using this method, without harm to the quilt or the fabrics. You must rinse with clear water after the marks are erased to get the juice out, but that's a minor price.
I use the Dritz water soluable pencils, also. They are good for my arthritic hands. :<)
Sharon