Missing items in Ultra 6 Plus GUI Menu

Well that is odd then. There's no reason why a computer accessing the NAS for the first time should see this issue if already on 4.2.16. Caching of the browser happens on the client machine not on the NAS. If you had restored a config backup from pre-4.2.16 if it included the apache config you'd see the issue but it would only be fixed by an OS Re-install.

There are a few possible reasons for why the unit shipped with 4.2.15:

1. NAS unit could have been produced a long time ago now and been sitting on a shelf somewhere (e.g. at the reseller)
2. You cannot downgrade from 4.2.16 to earlier firmware so it's possible that NetGear still produced units with 4.2.15 pre-installed for a long while after 4.2.16 was released for those users who preferred to use older firmware. NetGear recommends running the latest firmware.

I'd recommend you choose to use dual-redundancy. See http://support.netgear.com/app/answers/detail/a_id/19044/~/converting-and-xraid2-system-to-dual-redundancy