This is still the most suspicious one. I think muting a parent category can result in the subcategories being muted too. Are you sure no category is muted in your preferences?
If you filter latest for one of the subcategories that are missing on the unfiltered latest, which tracking state does the dropdown show?
I don’t think muting is the right way to enforce that. I’d try to use the category security settings for that. Only allowing reading on the parent category, but reading, replying, and creating in the subcategories should work to prevent replies to the parent. You might also want to enable default_subcategory_on_read_only_category. (I am not sure it matters that much now as the new topic button is no longer disabled on categories where you are not allowed to post.)
Don’t forget to use the option to change the preference for existing users when you remove the categories from the default muted setting.