What doesn't work:
This also happens with a generic scroll mouse, so it isn't specific to trackpads and probably isn't specific to any trackpad-centric settings (such as inertia scrolling). In fact, in my own case, the Magic Trackpad works fine 100% of the time.
PDFs seem to be affected the most often, multi-page PDFs as well. Altering any settings within Preview hasn't done anything to fix it except resize the window (see below).
What works:
Using the arrow keys, actually does work (as awkward as it may be) - Scroll bar doesn't show this way, though.
Scrolling left-right, by way of holding [shift] and using a scroll wheel actually does work - Scroll bar doesn't show this way still.
Resizing the window, that is, making it shorter seems to make everything magically work normal. If it is too long it won't scroll but after shortening a little bit at a time, it suddenly starts working normal. This is a workaround at best but it does allow for normal scrolling.
This is certainly a Preview bug that I doubt any of us can fix except by telling Apple directly. http://www.apple.com/feedback