I got the impression they got through painting a good portion of the 29K fleet fairly quickly, then it seemed to grind to a halt. I suspect the project ran out of money.
In general, train coaches need a repaint around every ten years as part of their general upkeep. The 29Ks are between 14 and 17 years old, so it's possible some had been repainted in the old livery, and won't need another repaint for a few years. Having said some of them look pretty rough, in fact some of the repainted ones could really use a bit of a touch-up.
I agree it has nothing to do with running trains on time. As the bodywork is mostly aluminium these days, I'm not sure painting them is even necessary, as it would be for steel bodies.