I've tested a second Mac (Mac mini this time) with an apple magic trackpad and an iMac with a clean OSX install with a Magic Mouse and all three computers and 4 input devices show the exact same asymmetrical behavior.
You are not able to reproduce it because the Apple Mouse which you have scrolls in small discrete movements (I have one and tested it and you are right this model does not have the assymetry) each of which overcome the scroll rate threshold. However, "continuous" touch scroll devices like the Apple
Magic Mouse, Apple Magic Trackpad, and any Macbook Trackpad all seem to have this problem and scrolling up is very disjointed. I've not seen this happen in any other program with any of these devices.
Here is a recording I made with the live input of my Magic Mouse scroll sensor displayed while I first scroll up then down and you can see the book area barely scrolls up until the third try when I go fast.
Interestingly, in the second half of the recording I then do the same up/down scroll in the Table of Contents area and there is no problem, it scrolls perfectly symmetrically no matter how slow I go. So this is a problem specific to the main text window only. The TOC right next to it scrolls perfectly.
