After healing the tube externally, I switched the power supply between the two clocks.
When putting the tube to the new clock, there were no dark patches, only discoloured ones.
The new clock was now brighter than the older clock.
The tube finished healing on the new clock after 1 day and the digit discolouration is now gone.
I always assumed it was a clock issue because I've used two different power supplies (after the initial one), but they seemed to have the same problem.
And when I took the anode measurement, I used the same power supply for both clocks.
So, the problem is clearly not on the clock, but in the power supplies.
I've now connected the old clock to a 3A heavy duty power supply and the brightness is also good now.
I'm sorry for not testing more extensively. Probably could have saved some unnecessary discussion.
Have you checked the waveforms out of the supply while loaded? On rare occasions, I have seen a power supply deliver superimposed noise that can drive a regulator chip on the load side crazy... The fix is generally easy - deposit the power supply in the trash.
It's not uncommon for cheaper power supplies not be able to deliver enough current.
I just assumed I have two like this out of a 6 pack I bought from China. That's a lesson never learned.
They are now both resting in the recycle bin.