Yes, that is wacky. At first I thought you might have been using the extended driver to send the book as a kepub, but then you wouldn't have the page number in the margin.
The only thing I can think of is that the book has a page map in it that is broken. Have you tried opening it with ADE? It would be interesting to see if it shows the same problems.
Is there any chance we can see the book? If it is somewhere legal to download, that would be good. Even looking at a preview might help.
Also, which Kobo device and firmware are you using?
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