I presume you did do the device setup via Kobo Desktop?
Where on your device are you placing the books? Do NOT place them in the .kobo directory, or ANY directory that starts with a period.
After you disconnect the device from your computer you should see a "Processing content" screen pop up on the Kobo.
Don't expect much joy from transferring MOBI format material. While yes, Kobo DOES have some support for Mobi format, I would not depend on it working well.
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