Finally I found out what the problem was we were facing. Although discarded as a theme problem, I don’t think it is. It’s a limitation of the plugin. Due to the fact the plugin can only have 1 form for Post Type Archive, we need to use the same form in different places. Let’s say I have category archives and taxonomy archives and I want the S/F to be placed on both. On the category archive I want the user to give the option to select different taxonomies and on the taxonomy archive I want to use different categories. In this case, hide empty terms breaks the plugin. It would be great if this would be fixed in the future.