Evernote support has provided a guide for me on how to work around a bug in Evernote 10 where notebooks appear to be duplicates.
Solution:
Change the "Display Language" setting in "Personal Settings" (https://www.evernote.com/PersonalSettings.action) to "English".
Same problem with Evernote 10.8.4-win-ddl-public (2349).
When I select one of the notebooks, other one will also appear selected. And when I deselect a notebooks, only one notebook will be deselected.