I have been following this thread as I am having the same issues - books that are throwing up recto where they should be verso etc, regardless of the page that the previous chapter ended on.
I have checked all the settings and have the auto numbering on and the auto chapter numbering as suggested.
I have tried having text on the page and having imagery on the first page and it doesn't seem to make any difference at all.
I am still clueless how to fix it. Maybe it is a bug, as I had a perfectly laid out book before I added in some change to the page numbering. Is it possible that the page numbering feature can be glitchy?
One thing I found that was messing me up was that I forgot to check all previous chapters - not just the one immediately before the one in which the pagination didn't seem to be working.
Do you know if all previous chapters "end" correctly?
As far as I know there are no glitches in the numbering algorithms. I'm going to branch this thread to it's own topic because your problem is probably different after two years. Please give us full details about your OS, the version of ID and the latest patch installed, and the document structure. Also some screen shots of your pages panel for the document, and for the Book panel, if this is a Book.