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Hopefully someone more knowledgeable will be along soon, but that sounds like maybe you are loading a "problem" book on, which your kobo can't process correctly. This is often because of bad formatting. The first thing I would try is to add one book, and see if it processes. If not, delete it, and try a different book. It is easier to find the problem book if you start with no books on your device, then try adding them on slowly.
However, when you say this only happens with Calibre, but is fine when loaded with Adobe, do you mean the same identical book? If so, it sounds more complicated, but if you mean different books, what I said above still applies.
Others will probably give better, more in-depth advice, but it's somewhere to start.
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