Let me add some background points to this discussion.
1) Avaya have a very comprehensive tutorial on VLAN technologies on their web site - have a look at . Start at about slide 21 if you already know LAN basics.
2) The terminology can get very confusing, partly because a lot of it predates standards. Cisco talk about native VLAN; the 802.1Q standard about PVID (port VLAN ID). These are separate from which VLANs are tagged on any particular port.
3) According to Avaya (I've not read the standard) 802.1Q defines three types of port: access ports where frames are not tagged; trunk ports where
*all* frames are tagged and hybrid ports where frames may be tagged or not tagged. Cisco trunk ports are hybrid ports according
802.1Q.
4) The usual Cisco behaviour on a trunk (hybrid) port is to send all frames tagged except for the native VLAN (PVID); all untagged frames received are noted[1] as belonging to the native VLAN, as are frames tagged for the native VLAN; other tagged frames are noted for their correct VLAN.
5) Just as a side note, 802.1Q inserts tags into frames to provide the VLAN information. Cisco ISL encapsulates the original frame with a new header containing the VLAN id.
HTH
Sam
[1] I use the word "noted" to mean that the switch internally keeps track of which VLAN a frame belongs to. How it does that - with tagging, encapsulation, a field in a data table or whatever - is up to its designer and is actually irrelevant to us poor users since we can't see inside the switch.