OK, I have a theory about how this thing is behaving; bookmarks seem to show up/behave as you would expect (when I tap on the ribbon) provided I have the font size set to something that appears to paginate the book to its original (just a guess on my part) layout. If I increase the font size to make things larger/more easily readable, then things get screwy as described above as the pagination bumps up the # of pages and the page #s where a ribbon gets place doesn't seem to correspond to the exact visible page I wanted it on. Confused? So was I, but the evidence seems to point to this.
Anyway, try this out and see if it doesn' behave as I described.
Bottom line - iBooks does not behave in a rational manner and therefore it is buggy in my opinion - i.e. this is not a "feature"...
I have no experience with other iBooks downloads. Steve Jobs is my first purchase - and this this is my introduction to iPad and iBooks and terribly ironic to discover behavior like this with the ode to Steve book - which, BTW, I am enjoying max.