I tried this several different way and am now pretty convinced there is a bug, or some major instructional step we are missing.

Basically, the filters don’t work with Custom Post Type + Custom Taxonomies.

All of the custom taxonomy filters incorrectly report zero results.
http://ccgrow.wpengine.com/
(The regular category filter works fine, I just left it there for testing).

We definitely have some custom taxonomy results (zones), as shown here:
http://ccgrow.wpengine.com/zones/1a/

And we definitely have some custom post (plants), as shown here:
http://ccgrow.wpengine.com/phytotheca/

Other notes – I tried the following things and got the same results:
– implementation locally
– implementation on production
– hand-code custom post types & custom archives
– use Custom post type UI to create custom post types & custom archives
– implementation in a custom theme
– implementation in the 2014 theme
– various widget configurations

I also tried working with the free version, and ran into some different problems there. (Filters would work, but the results page would not correctly display the active filters)

Thanks in advance for your help (when you get back). I can tell by the forum that you have been very proactive about working with people on this.