If you create a new custom orthotropic material as you are used to, it will ask you for a reference plane.
If you create a new custom orthotropic material in the composite menu, it doesn't need a reference plane, because it will use the surface geometry as a reference. This orientation you can see in the preview of the composite material, and you can edit it (per face) in the composite menu.
When you open the material library, the default settings will show you isotropic options. After you set it to orthotropic and select a reference, it will remember the settings on this part. If you use your custom material again in another part, it will start with isotropic properties again, and you have to change it again.
It is quite predictable, but you need to keep your workflow in mind.