Hi Ernest
I’m not sure I understand why the staging version of the site, with the older plugin running, works with the same settings (or what were the same settings before you tweaked the live version ones while looking into this).
On staging:
http://unicorngcb.staging.wpengine.com/catalogue/
a search for ‘proposals’ will produce results with all checkboxes selected.
On live:
http://gcb.worldanimalprotection.org/catalogue/
the same keyword search with the same checkboxes selected will not.
Essentially, the staging version of the plugin / search works fine, but the live version with the newer plugin installed does not behave the same way, with the same contents.
Best
Paul