LEDs intermittently non-responsive to short multiplexed pulses after high reverse voltage?
The culprit was mechanical damage to the connections from the legs of the LEDs to their diode crystals.

I bent the legs of the LEDs at 90 degrees without without support which caused mechanical damage which manifested itself in these intermittent failures.

Thanks to Ian.M from the EEVblog forum for pinpointing the issue for me!