Well, after all of this, I agree that the clock is running as designed and that there is nothing that can be done in the software to increase the brightness (sorry about my learning curve for multiplexing!). A few more comments and thoughts:
1. I do have an Ian Arduino Shield IN-14 clock that has been running for years at this point. It is also a multiplex design. Putting the IN-8 clock side by side with it in a somewhat darker room, I cannot detect any difference in brightness. So for a clock located away from bright light, it is just fine as is.
2. I've now gone ahead and increased the target voltage of the IN-8 clock from 180 to 195 and that has increased the brightness a noticeable amount. I now show 4.25 volts dropping across the 3k resistor for a current of 1.42 ma. How much higher can the voltage be pushed with this design?
3. I do wonder a bit about the tubehobby datasheet. There are several "recommendations" here. For example, the one about keeping anode current to 1 ma at 180 volts. Is this referring to supply voltage? Also, Nixie tubes seem quite tolerant of higher currents over short periods of time (hence Ian's tube healing mode). Any additional clarification here would be appreciated.
Also, I've been running an IN-18 clock from GRA&AFCH for about 8 months now. It's a direct drive clock with a 180 volt supply. The interesting thing about it is that the anode resistors are 1k. I measure about 5 volts across them which is also 5 ma. The sustain voltage for these tubes is about 130 volts. So GRA is pumping about 50 ma through the tube with a 10% duty cycle (using a timer to control this) on a normal basis. There is an interesting write up
here
In any case, it just makes me wonder if some of the tubehobby recommendations aren't a bit conservative..