Taxonomy term: "The requested page "xx" could not be found."
I will answer my own question on this one:

On a site that has several vocabularies, enabling the selection of one of those vocabularies in the contextual filer of the default taxonomy view, removes the paths assigned to the terms of other vocabularies (those that have nothing to do with the view.) Those paths then default to the root directory and the term pages can no longer be found (or used in another view, etc.)

Un-selecting the vocabulary returns functionality to the term paths of other vocabularies but also allows the existing view to be displayed on all vocabulary term pages (this appears to be functioning as designed however.)

It appears to be a bug in the taxonomy module for which there is no fix. :(