This morning I was reading a section from Church Dogmatics,
I noted that it was particularly slow to scroll, the first few lines would scroll ok, then it would skip haphazardly with 1-2 second pauses before scrolling again. Bizzarely, the problem was not isolated to just CD. While CD was open, all other resources also scrolled equally poorly - and then went back to normal when CD was closed!
This is is what was happening to the CPU with jerky scrolling in CD, it was similar with scrolling in other books while CD was open:

Basically that represents one (of two) cores being hit at 100% by L4 (orange line) while scrolling.
This is what it looks like if scrolling normally when CD is not open:

Very odd, I'm away from my other system so I can't test if it's just this computer or if it's something to do with Church Dogmatics; for the moment I've discovered it's smoother to read CD via 3G on my iPhone than on my laptop off the hard drive [:D]