With those results:
- Remove all the books that haven't been processed by the device
- Copy one epub over without calibre. Makes sure it isn't one you just removed.
- Disconnect the device and see what happens.
I don't know why I didn't think of this yesterday, but what might be happening is that you have a "bad" epub in there. When the device is disconnected, it processes the books and adds them to it library. But, if the device can't read an epub for some reason, it stops the processing and doesn't add any more books to the library. If this is the problem, you have to go through the epubs one at a time to work out what is wrong.
The above is based on how the Kobo Touch works. I'm pretty sure the other Kobo's will work in a similar way.
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