I searched and found quite a few articles, but nothing has quite answered my question yet. I am working with Commerce.

I am creating views that filter my products onto different pages. In short, I have created one taxonomy (Portal) with three terms to categorize the products into either or both of the views, and I have created a second taxonomy(Category) to filter that product into four different views within the first one. I hope that is clear enough.

I will skip a lot of steps to make this post as succinct as possible

First, I have added both of the taxonomies via the term reference field type in th content type.
http://i.imgur.com/R0326LH.png

Second, I have added the "Category" taxonomy reference to the view's Filter Criteria and it works perfectly. The products have been configured at this point.
http://i.imgur.com/TpoX02R.png

Now when I go to add the next taxonomy reference for for the "Portal", it tells me that nothing is there?
http://i.imgur.com/T9WizCG.png

To contrast that, this is what I get for "Category"
http://i.imgur.com/vCnqSRt.png

I have gone through the setting for the taxonomies and the fields in the content type, and I can not find any differences (hopefully I am overlooking something.) I have also cleared the cache multiple times, used the rebuild taxonomy on submit option, re-indexed the search API, and ran cron.

Can somebody please tell me what I am missing? Would this module be helpful?
https://drupal.org/project/term_search

edit: I have realized that the taxonomy does not show up in admin/config/search/search_api/index/product_display/facets. Could that be the issue?

Ideally, I want to have "Indexed Node: Portal (= Both or Classic)" as the second item in this list.
http://i.imgur.com/b80eRtj.png