I've connected 3 x 3560 switches in a lab. Switch 1 is in VTP server mode and the other 2 are clients and the VTP domain is working fine.
On switch 1 I have set the trunk to switch 2 to use native vlan 99 and on all the other trunk ports on each switch I have not set this to purposely create a native VLAN mismatch. I have created VLAN 50, 60 & 70 on the server switch (switch1). Now I would assume that if there is a native VLAN mismatch on the first trunk between switch 1 & 2 then the client switches 2 & 3 wouldn't get the VLAN info created on the server switch? I have put a PC in VLAN 50 on switch 1 and switch 3 and they can ping each other.
And I misunderstanding what the Native VLAN does?