I agree with Tartan's thought. It doesn't seem like it's the thread color bleeding. Color is probably bleeding from the backing and adhering to the thread, coming through the needle holes and going onto the thread. Especially with the example listed of the daises turning pale blue in the center, which sounds like they should have been white because of the white thread and white top-- making it obvious in that case it's the backing that made the thread and top surface blue.