Do you see duplicate portlets in your environment after upgrading your Clarity? Have you flushed cache and restored defaults but to no success?
It has been found that Clarity upgrades will intermittently result in duplicate portlet displays. These duplicates will not be functional and will not be displayed in the Actions -> Configure menu from the Home side.
Publishing the portlet itself (not the portlet page containing the portlet and not the tab containing the portlet page) generally resolves the issue.
Please open a CA Support case if publishing the portlet does not help resolve the duplicate issue.