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This has to do with the Table of Contents and the way files are formatted internally. Epubs (and kepubs) are basically zip files with a defined structure of files and meta data inside. Kobo requires that each file inside the epub has a Table of Contents entry for the progress tracking and page count to work. For the vast majority of books, they split the files at the new chapters, so this just happens to be exactly the case.
However, some books, either because they do not have a table of contents, or files are split to create a page break, (say, for example, if there are full page illustrations withing the chapters.,) then the progress will not show properly (until someone edits the table of contents in Calibre. Calibre has a built in function to generate a new ToC based on files.)
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