I have had this issue several times now. I have a multi-chapter book. The page numbering goes like this: first chapter 1.1, 1.2, 1.3... next chapter 2.1, 2.2, 2.3, etc. I did that using Section Prefix and checked "Inlcude prefix..."
When I create a Table of Contents, it brings the page numbers in as 1,2,3, etc., thereby dropping the chapter prefixes. WHY? The numbers display correctly on each page, as well as in the InDesign Book window.