This thread is resolved. Here is a description of the problem and solution.
Problem:
The issue here is whenever the user creates their taxonomy in Types their menu disappears from the frontend and its no longer there in the Appearance -> Menu option.
Solution:
The problem was identified with the use of the slug "output" when creating a taxonomy. What seems to be happening is that 'output' might be an unlisted reserved word for taxonomies.
It should be noted that the problem also occurs when the taxonomy is created using PHP code and when the slug 'output' is assigned.
The user was advised to open a ticket with wordpress core because the issue is not on Toolset side but it's strictly with the wordpress core.
The issue need to be addressed by wordpress directly.
This is the technical support forum for Toolset - a suite of plugins for developing WordPress sites without writing PHP.
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