That's just how Sony renders epub. I don't know if it's reading the Adobe page-map extension in the .ncx file in the epub or if it's calculating the paging itself. See if your epubs page a pageList entry
in the .ncx and maybe try removing that?
If you're not aware, epub files are just zip files. You can rename a .epub to .zip and then open it with your favorite zip archive tool. You can then change contents manually, rezip, rename .epub and you'll have an edited book.