In calibre, what options do you have set for the Kobo driver? Easiest way to see is with the kobo attached, click the arrow besides the Device icon
and select configure this device
With me, if I have "Show Recommendations" selected I see one extra book, which is in collection Recommendations, and when I try to copy it I get a virtual book message.
So try disabling Recommendations in the driver.
And LOL.. If I also enable Previews I see a HECK of a lot more virtual books