URL Alias Preventing a Pattern on Vocabulary
Ok thanks to Digital Fire, I started checking for other alias conflicts, which I found in my defined views.  The problem I had initially was that the URL alias was working with views, however clicking on the link / taxonomy term took you too the default drupal view.  

So in order to get the term with an alias working with view's I realised that in the view path use the original link to the taxonomy term instead of the url alias.

Hopefully that makes sense and might help someone else out.