Most of what you described can be attributed to older firmware versus new manual. You can probably run just fine with the older firmware but updating to the latest would give you the missing features including the rather useful Over-The-Air updating. I don't find myself updating clocks very often but when I do it's nice to have the OTA.
EDIT: The OTA feature, in its present state of development, provides OTA updating of the ESP WiFi module but NOT the clock controller. So you still need physical access to the clock to update the controller.
Remember: you have to update the clock controller and the ESP at the same time. If you don't you end up with a version mismatch that can cause all kinds of troubles.
The time zone business is also a matter of versions. Your older version uses "tz database" aka "Olson" time whereas the newer versions use the more familiar NTP. I believe the manuals now talk only about NTP. Here is the URL to use for getting NZ time from Ian's tz server:
http://tzs.nixieclock.biz/getTime/Pacific/Auckland
For a complete explanation of tz / Olson time and a listing of all the various timezone URLs try here:
en.wikipedia.org/wiki/Tz_database and
en.wikipedia.org/wiki/List_of_tz_database_time_zones
Should you decide to update to the newest NTP-capable firmware, your Posix-style timezone string will look like this:
NZST-12NZDT,M10.1.0/2,M3.3.0/3
The module will automatically use pool.ntp.org without you having to do anything besides setting the timezone string.
Regarding the neon separators, I've seen something similar happening before. Neon lamps in general are not real happy being dimmed and there's a lot of variation between types (or even batches) of neons. As you mentioned, using LDR in a dark room exacerbates things. As an added complication the striking voltage of neon lamps inherently increases as the surroundings get darker.
Increasing the value of LDR Min DIm, or turning off Use LDR completely, may help but the obvious side effect is that the tubes don't dim as much. Sprinkling uranium ore on top of the clock will also help (just kidding, don't try it, but it is true that low level radiation improves neon devices' ability to strike in the dark, thus Kr-85 or Ar-42 gas being added to some Nixie tubes during manufacturing). Or you could do as I did and modify the firmware to make the neons blink instead of pulsate.