As I find it a very unintuitive way to set the "Port Native VLAN" on a Brocade switch, I just want to share this with the world. And this is how to set the "Port Native VLAN" on an interface:
interface ethernet <your interface>
dual-mode <native vlan>
!
If you don't specify <native vlan>
then the default VLAN (usually 1) is chosen.