Thanks, but that actually made it worse. Now I can't scroll with all chapters closed!
The technical support said, "I have looked into your notebook and I was able to reproduce the behavior you described on my Windows machine. As such I have filed a report with the appropriate development team so that they may further review the misbehavior.
You should be able to workaround this behavior by actively closing more cell sub-groups. For example, if every group in the notebook was opened, I was able to reliably reproduce the scrolling issue with your Applied Mathematics section. If I closed the subsections within it (Differential Equations, Integro-Differential Equations, ..., Mathematica Models), the notebook scrolled as one would expect.
When the scrolling issues did present themselves, I was able to workaround the issue by manually dragging the slider on the scrollbar. This seemed to be the only thing that worked in this situation.
We are always interested in improving Mathematica, and I'd like to thank you once more for bringing this issue to our attention. Please do not hesitate to contact us with any further issues you may come across."