I've figured out what the problem is. If you pin the Calibre icon to the taskbar using the icon that's there while Calibre is running, you won't see two icons. You will only ever see one icon. But, if you right click the Calibre icon from the desktop and select pin to taskbar from there, it will work.
When you pin from the icon when the program is running, it uses the same icon. When you pin from the desktop, it uses two different icons. Problem solved.
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