You simply have both 32 bit and 64 bit versions installed (a valid configuration BUT only if they are BOTH 5.x).
The BOTH use the same Library and settings BUT SHOULD NEVER BE RUN TOGETHER (the reason they now need to be 5.x)
You should uninstall the x86 version as it is NOW incompatible with the 5x library.
BUT Simply remove the shortcut from the desktop, then launch Calibre 64bit from the start Menu (then you should right click the taskbar and create a new desktop shortcut
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