doesn't work with custom taxonomy_term view

I have been using this module for a while now - and its been working great.
Now, however, I wish to alter/override my "taxonomy_term" view (which is preset in the views overview). I clone this view to override the standard setup and change the following:

Teaser view -> List view
Add Field -> Node title (as link)
Add Field -> Taxonomy: All Terms (as links)
Add Filter -> Node type -> restrict to nodes of type "Page" and "Story"

In my new view, the terms from my permission restricted vocabulary along with the terms from my non-restricted vocabularies. :(

All help will be very much appriciated!