This is the worst 'feature' I've ever heard of!
The Kobo already displayes the page number, there is no need for it to be duplicated, especially since it overlaps the book's text. It really does look like a glitch (and until now, I assumed that's what it was).
EDIT: Found these instructions on the intertubes, not sure if they work at all, as I'm at work right now and can't test...
There is a way but I don't know, if it makes any sense to you.
its as follows:
1. Add page-map attribute in the OPF file.
2. remove the page links from the pagemap.xml file (if exists any), so that
ADE will not find any page numbers to display.
3. Then make an ePub out of it.
The page-template file does not control the display of page numbers.
What you're looking for is the page-map.xml file.
Go to http://www.adobe.com/devnet/digitalpublishing/ and download the
"EPUB Best Practices Guide". There's a section on "Adobe Extensions"
which discusses the page map file. To suppress page numbering, you'll
need to create such a file, but use an empty name attribute (note that
I haven't tried this). If the page-map file doesn't exist, ADE will
generate page numbers based on the algorithm discussed in the best