Combination of things, but mostly a serious infestation of gnats. It is possible that the soil itself had issues, but I will never know. At any rate, I got tired of killing seeds and chasing gnats, so I moved on. I may do another attempt at KIS soil at some point, but I ran out of time and patience this time around. I doubt that there is anything wrong with soil in autopots as long as one keeps the soil mix light with perlite, especially in the flood zone of the autovalve, but I will not be testing the notion this time around.
So far, the replacement grow is going perfectly, so perhaps I will make the SS#4 work better. I will at least not have to fight with the bloody gnats from the get go.