PX SEO uses the URL Joomla builds for the article, and with two Single Article items Joomla has two valid URLs for the same page – which one wins depends on where the link is built. The clean fix is to keep one URL: change the footer item's type to Menu Item Alias and point it at the main menu item. The footer link stays, it just uses the main URL, and the canonical follows.

Makes sense. The footer item has its own page title and meta description though – do I lose those with an alias?