With these type of VLAN settings you can also use the switch port General mode instead of trunking mode. General mode allows you to be more specific on creating the vlans  and setting what you want to be the native vlan and what you want to set as the tagged vlans.  I recommend to not use trunk mode if you want to specifically assign native vlans beside the default vlan 1.    The issue you have shown here very well could be an issue in the firmware. To properly document this issue I would suggest calling into support at 1-800-945-3355, Where a case can be opened, documented, and escalated if need be.  Thanks.
Firmware version: 4.1.0.8. This is how to reproduce the problem: 1) configure 802.1q trunk with native VLAN other then 1, for example: interface gigabitethernet1/0/1 switchport mode trunk switchport trunk native vlan 30 switchport trunk allowed vlan add 30,1012) save switch config on TFTP server or locally via HTTP in the saved file VLAN configuration on interface looks like this: interface gigabitethernet1/0/1 switchport mode trunk switchport trunk native vlan 30 switchport trunk allowed vlan remove 1-29,31-100,102-4094 3) load saved configuration as startup-config check loaded config ('more  startup-config'): interface gigabitethernet1/0/1 switchport mode trunk switchport trunk native vlan 30 switchport trunk allowed vlan none As a result interface is not operational. If you edit saved file like this:  interface gigabitethernet1/0/1  switchport mode trunk  switchport trunk native vlan 30- switchport trunk allowed vlan remove 1-29,31-100,102-4094+ switchport trunk allowed vlan add 30,101 configuration is loaded correctly. This looks like not completely fixed bug from 4.1.0.1 when you were getting 'allowed vlan none' also in case of native vlan 1.  
PowerConnect 5548: incorrect VLAN trunk configuration when loading config