I recently built a Rev.4 classic nixie clock and got everything working with IN-12 tubes. But from the day i powerded it on, it has lost about 4 minutes in about two days. Unplugging the power doesn't change the time (obviously, it's designed to keep the clock running)
When i cycle through the temporary displays, it says that the RTC is conected - (11) and temperature is at 25 C*.
The only modification i made to the RTC is that i unsoldered the charger circuit resistor (because my CR2032 where bulging out).
There have been some reliability issues with the RTC modules over the years, it seems to come and go, I suppose as the factory goes through manufacturing challenges. Losing 2 minutes a day sounds a lot like the internal drift of the crystal oscillator. Contact me and we'll exchange it.