[New Blog Templates] New Blog Template Not Copying over Taxonomies

We are running New Blog Templates in our environment to allow users to create new blogs with specific themes and settings.

Our environment includes a multi-site, multi-network installation running WordPress v4.9.6 with PHP 7.1.1 on RHEL with Apache 2.4.

We store all our templates in the root network (wp.odu.edu) and use New Blogs Template for users to create sites on other networks using them.

This has worked really well until recently when we were trying to track which templates were used most. We added both Tags and Categories to the template sites. We also went into the New Blog Template and made sure that the check box for tags and categories was checked to copy them over to new sites.

We ran a number of tests with various templates and the tags & categories are not being copied over to the new sites.

Any suggestions?