When you use calibre, how many books are you sending to the device? If you are sending only one, then taking hours is bad. But, if you are sending thousands, then hours is reasonable.
As @Uschiekid said, books with errors in them can cause problems. And can block importing books found after it.
One question, what firmware version are you running? Older firmware was a lot slower to import books and had more problems doing this.
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