I’m sorry, but this discussion doesn’t move forward. I feel that you hide information each time you say something. KiCad behaves in a well reasoned, logical way, even though it’s not the easiest possible to understand. You tell about new problems (now 3D) without giving us enough information to solve the old ones.
The FAQ section has enough information to solve these problems. I understand it’s too much in a short time if you don’t understand the details already. But have you tried to understand how the library system works? If you do understand it, I believe you can solve these problems without our help. I believe there’s nothing strange going on with your setup.
If you’re not willing to invest time to read and understand the relevant FAQ threads, at least give us what you’ve got on your system. I already asked for screenshots. Another option is to give the content of the configuration directory (Rene gave a link to information about where that can be found) and maybe some example project (the contents of the directory) which is problematic.