I recommend not using calibre and the Kobo desktop application in the same connection session. It should be OK, but, I had some problems early on and now avoid it. Running both at the same time is definitely a bad idea.
Unless you are syncing books with Kobo and don't have WiFi, the desktop app isn't very useful. About the only time I use it is after a factory reset and if I wan't to remove a lot of kepubs from the device. The app is better for this than the device UI.
I usually eject from within calibre. Then I make sure Windows has ejected it before disconnecting. And to make the eject easier, I use the SmartEject plugin to give me a nice button to press. That has some other options, but I turn them off.
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