We report on a large-scale study of student learning of quantum tunneling in four traditional and four transformed modern physics courses. In the transformed courses, which were designed to address student difficulties found in previous research, students still struggle with many of the same issues found in other courses. However, the reasons for these difficulties are more subtle, and many new issues are brought to the surface. By explicitly addressing how to build models of wave functions and energy and how to relate these models to real physical systems, we have opened up a floodgate of deep and difficult questions as students struggle to make sense of these models. We conclude that the difficulties found in previous research are the tip of the iceberg, and the real issue at the heart of student difficulties in learning quantum tunneling is the struggle to build the complex models that are implicit in experts’ understanding but often not explicitly addressed in instruction.