The problem with the fonts was apparently not with every book. But for the book I'm reading right now, The Round House by Louise Erdrich, I did find differences with my Kindles. On the paperwhite, I don't like the font it's in, which I think is Helvetica, but I'm unable to change it to anything else. The KPW is on version 5.3.1. I was able to change the font on another book I got recently. Maybe I'll try the update this weekend and see if it will fix the problem. I just realized I also read the title of this thread wrong, and thought at first this was a follow-up update to the recent Kindle Touch update. I only just realized there's actually a new paperwhite update as well. (even though this is of course clearly stated in the thread title!)
I'm reading The Round House on the Kindle Touch instead, because I can still change among the available typefaces there. Right now that's on 5.1.2. I think I'll try the KPW update first, and see if I can change the font on this book after that. Otherwise, I think I'll wait until I finish reading the book before doing the K Touch update. I am looking forward to having the newer features on the K Touch, though.