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There is a issue where kobo is being "interpreted" to be another application. I had the problem where my iPhone was plugged in. I resolved the problem by un-installing iTune app. Somehow windows os associated kobo to be some other device or just open file folder only. Some other background process intercept the kobo startup and prevent it from being recognized properly. Had a problem with my Calibre as well - where it could not recognize kobo. I have also turn off the Calibre plug-in for iTunes.
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