Usually ePub files are organized in a series of XHTML files, one per chapter or section. So it sort of makes sense that when you need to load the next chapter that there would be some sort of reset going on, requiring a 'flash'.
When I played with one at the store, in fact, I never got the advertised 6 pages of flash free page turns, and I tried several different books. It seemed more random.
I actually think the attempt to eliminate 'PTF' is doomed to failure or at least lack of success, maybe even just a marketing gimmick. Given the way perception works, it is much easier to ignore something that happens predictably and regularly, as I have on my Kindles over the last couple of years. Not sure 'intermittent' flash will be as easy to ignore. And if it leads to 'ghosting', get rid of it please! But only time will tell, my new nook is waiting for me in its unopened box at home and I'm looking forward to using it.
On one of the Kobo forums they were discussing the same issue, and apparently Kobo intends to make the flash frequency configurable by # of page turns in a future update. Again, I'm not sure that will work well unless it is a simple "attempt to suppress PTF: yes/no".