What you're describing sounds like an intermittent bug in the software thats been around since the release of the NST. Because it is not reliably reproducable a patch to fix this has never been issued.
This only affects the home page. If you restrict accessing books to using the Library View you shouldn't have problems with bookmarks or the last page read.
Have you tried taking it to a store and having them look at it? In any manufacturing process there are going to be some that don't work properly from the start and need to be replaced. I know it's disappointing to wait for something and have it not work properly but this not the norm, otherwise there would be thousands of posts complaining. Before getting mad take it to a store or call cs, they may just replace it. Also, out of curiosity have you tried completely powering it off and on. Not just putting it to sleep but a complete power down.