If you have newest Kobo Touch firmware, have you done the setup already (with registering with Kobo)? It is required step or sideloading books doesn't work.
There is workaround for dummy registration if you want to skip it. I just don't remember in which thread it is...
If you have registered your device, then it might be that your device database is somehow corrupted (it should automatically add your books to library when you disconnect the reader from computer...). You might reset it to factory defaults. This will delete the books and database and starts over from beginning.
Edit. Instructions are here:
https://www.mobileread.com/forums/sho...&postcount=262