I too, wondered what caused such significant losses. Apparently the pre-emergence chemicals put down at the time of the planting (to supress the emergence of unwanted weeds and grass) gravitated downward and stunted or prevented the cotton seed from germinating. Excessive rains could conceiveably have contributed to the problem.
All this is speculation on my part; not having grown cotton since the early fifties before pre-emergence chemicals were used. Back then, the grass that sprouted among the cotton stalks had to be removed by hand, using a cotton hoe.
Actually, I think that part was about why the milo that was an attempted replacement crop wouldn't grow.
The article does finally get around to saying that the reason the cotton isn't growing is because of the storms, but through the first part, I couldn't figure out if it were drought, floods, insect plague, or disease.