See
this thread. It's how e-ink screens work. The firmware has settings where you can set it to refresh from between every page up to once every 6 pages. You can set it to do the total refresh less frequently by editing a file, the instructions are in Post #5 of the thread.
Setting it too infrequently can result in seeing some ghosting of text, you'll have to see what works out best for you. Mine is set to refresh after 50 page turns, and I don't really see any ghosting other than on the cover when I turn it off.
Edit: Meeera typed faster!

And the flash never bothers me at all even when it does it every page turn. It's certainly much less disruptive than if you were turning the page of a book.