Can't really comment on the no results problem.
However, the Taxonomy View renders as a page, so no you can't have both the original view and the cloned view enabled at the same time and expect them both to override taxonomy pages.
The only way to have both enabled is to set a different path for each view, which means one or both views would not override taxonomy pages at all.
If what you want to achieve is overriding taxonomy pages for terms of specific vocabularies, what I did was use the Disable Taxonomy Term Listing module to completely hide results of the normal taxonomy page, then replaced that content with taxonomy block views. If this isn't what you are looking for then feel free to disregard this all ;-)