I’m running version 4.5 stable, but I’ve had this issue in previous versions of the engine too.
Sometimes a seemingly random MeshInstance3D will refuse to update its cull mask values from the editor; the editor interface will show the correct cull mask values, but it will still use the default cull mask ingame. The only workaround I’ve found is to call set_layer_mask_value() in the object’s _ready() function. Any ideas what could be causing this? It’s not a huge deal as I have a workaround, but it’s been bugging me.