Hello Terry
The behavior you are describing is expected. Many control protocols still use VLAN 1 to exchange information even if you change the native VLAN to a different value. This includes VTP.
The point of changing the native VLAN has to do with protection against attacks on the data plane. This mitigates against VLAN hopping attacks, switch spoofing, double tagging, man-in the middle attacks, VLAN leaking and others. All of these occur on the data plane.
If you want to protect control frames that use VLAN 1, there are other options including the isolation of VLAN 1 (i.e. don’t use it anywhere else), as well as Control Plane Policing (CoPP), and VACLs. Some protocols, such as CDP and STP have their own security features that you can enable to ensure they are not compromised.
I hope this has been helpful!
Laz