I have no idea but you could try the following:
Check what book format your original PDF was in after it reached the Kobo? Close Calibre and connect the Kobo via USB to your PC (or Mac). Use your PC operating system to search the Kobo file system for the book's name and check the file extension. Is it still .pdf?
If I had to make a guess I'd say that your source book is a PDF with multiple columns and that it has been auto-converted to epub (or kepub) during the Calibre send-to-device process. Calibre does not convert multi-column PDFs well.
If you find that your original .pdf book has become .epub (or .kepub.epub) on the Kobo then you need to have a look at the configuration of your Calibre Kobo driver (KoboTouch or KoboTouchExtended). The 'File Formats' tab shows a list of what book formats can be transferred. Make sure the PDF box is checked. If you do not have the PDF box checked then PDFs will be auto-converted during the Calibre send-to-device process.
... or I may be on completely the wrong track
