When the KoboTouchExtended driver does not send a book as a kepub, it means that there is a problem with the book. It could be DRM or something unusual about the structure of the code in the book. As you have converted from PDF, it won't be DRM.
The problem with the book that the driver is seeing might not be something that affects other uses. It might be something the driver hasn't been coded for or some sort of strange characters in the book. But, there should be errors when this happens. There are a couple of options in the driver to keep sending the books if the conversion fails. I assume you have these turned on. Turning them off should show more information.
Other than that, I suggest looking at the
thread for the driver. The first post has any limitations on the driver and how to report bugs.