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You don't have both instances of Calibre open at the same time do you? Don't know if that's causing the problem, but it's generally considered important to have it only open on one PC at a time with a setup like you're doing. I don't have a Google Drive setup, but do have mine setup with Dropbox (home & work PC's) and it works great, no problems with one or the other not seeing all the books.
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