I'm having a similar problem: ipad nook app does NOT sync up last page read to the nook, but the inverse DOES work.
I have an ipad runing IOS 5.1.1 and nook app version 184.108.40.206. I also have the newest nook simple touch with background lighting. I use both devices for reading.
- when read on my nook previous time, I go to ipad app; it tells me there is a new page for the book I'm reading, I'm promted with option to go to that page and it works without issues.
- when I read on ipad previous time, I go to my nook and it never even aware of a new page to sync up to.
Retrieving data ...