Here's the scenario....
Reading a book. Maybe its contents have chapters, maybe they don't. Anyway, I bookmark the beginning of chapters or things I want to go back to. Let's say I bookmark page 10, 20, 30, and 40. Then I realized I don't need those any longer, so I clear them. Then I bookmark pages 60, 80, and 100, stopping reading on page 105.
So then I leave the book, maybe read another book for a bit, then come back to the book with all the bookmarks. Opens to the cover, not where I stopped reading. Really annoying. But, okay, I've been adding bookmarks! So I open up the bookmarks and there they are for pages 10, 20, 30, and 40 -- the ones I deleted and none of the newer ones.
I've sent this in to B&N technical "support" and they spewed back to me a default cut-and-paste, catch-all answer of "turn your Nook off and back on." Yah, right. So I decided to humor them and try it. Still happens, as I knew it would. So now I know to never contact B&N technical "support" because they haven't a clue.
No rhyme or reason to it. Sometimes they work and hold. Sometimes they don't. Just spent 15 minutes trying to find where I left off in this one book because it had bookmarks for pages 46 and 86 and I know I was somewhere in the 200s when I left off.
Workaround: a Post-It note inside the cover of the case where I can leave a note of where I stopped. Stupid, I know, but it works better than the Nook's bookmarking feature.
Hah. I was just googling to see if anyone else had complained because I have essentially EXACTLY the same problem.