Hi Lewis
I had a look.
So stage1 is working fine, but stage2 has count issues.
Something like this (where the counts are broken, but the search still works) is usually the result of something modifying our query for generating the counts.
In my experience, this is usually a filter in the theme, like pre_get_posts
that modifies our query when it shouldn’t.
To find out where this comes from I would:
1) Look at all the differences between stage1 and stage2 (plugin combinations + versions, theme version)
2) Start disabling things to find by process of elimination where the issue is coming from, I would start by testing on another theme, then try the plugins
Once we know exactly where the issue is coming from, I can investigate how to overcome it.
Best