Hello Andy,
first of all the native vlan is an OSI layer 2 concept:
the interface that you see shut down is the L3 interface that can be associated to broadcast domain Vlan1 (it is an SVI switched virtual interface).
vlan1 should still the native vlan even if SVI vlan1 is shut.
to verify what are the native vlan settings you can use:
sh int type x/y switchport
look for the native vlan line
about interfaces:
sh int ?
see if the other interfaces are fastethernet
Hope to help
Giuseppe