@AllanMcPherson you may have surreptitiously stumbled upon an interesting scientific principle here.....!
First, corn cod is a seed pod. Each kernel are genetically different because they are seed for the next generation of plant. we tend to think that each kernel is a clone of the plant because they are all the same colour but it is clear by looking at Indian corn that each kernel is different
The varying colours of Indian corn is mostly due to zeaxanthin content
Now, one fundamental principle of natural colour chemistry is that these compounds are unstable because they change colour with heat and pH. I noticed you added Mirin which is acidic. I would bet that the long slow cooking and mild acidity acted upon zeaxanthin and chemically changed it's characteristics and shade according to the content in each grain. Lutein, another pigment could be also involved.
another hypothesis is that you have hacked the cellular machinery of the corn kernels with your conditions and the results was a complex regurgitation of colouring mistakes because Zeaxanthin and Lutein are xantophylls, a class of chemicals are very similar yet come in a wide variety of colours (yello-orange-dark red to green).
either way, cool experiment!!!