This can happen if there is a fault in the book's TOC.
The KEPUB reader especially expects the NCX toc to be in a very specific form, and all sorts of things will break if it is not, including the page numbering. The EPUB reader is not quite as strict, but it expects at least the order of entries in the NCX toc to match the order of the OPF spine.
Edit: if you want to post the OPF and NCX files from one of the books that has the problem then I'll see if I can point out the faults.
Last edited by GeoffR; 07-15-2015 at 01:24 AM.
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