I think I've found the reason why JB couldn't detect newly transferred ebooks.
This problem only occurred when I plugged my JB to the PC's USB port when the JB was either displaying a page of an ebook, or the book list.
The solution is to go back to the main menu (where folders are displayed) before connecting the JB to the PC.
Although I have 2 ebook readers now, jetBook is the one I use all the time.