Hey there
Just to let you know support is a bit limited right now until after the new year break.
Anyway, I had a look.
Typically, you should be specifying your custom template for displaying your results – this gives you control over what is happening.
When you don’t specify a custom template, then you are really at the mercy of WP which file is loaded.
In your case, it seems that the template file that is loaded automatically has some code on it that is modifying your queries, and probably the S&F query too – which is causing problems with the count numbers.
I see from you screenshot that there is only 1 field where the count numbers are a problem – which to mean indicates again, some custom code like pre_get_posts
or something similar.
I also tested on the default 2015 theme here quickly, and changing this setting has no effect on the count numbers.
I would look carefully at the template file that is loaded, and see how it might be using some greedy code or filters that are incorrectly also being applied to the S&F query.
The correct approach would be to create a new templated, based of say search.php
specifically for Search & Filter. Then you could copy the layout from the other template into here, ensuring you are not copying over any filters etc that are causing the issue.
Hope that helps!
Thanks