As you might recall, I had a fair amount of experience with the spotting phenomenon in the course of the thread at http://www.pizzamaking.com/forum/index.php/topic,3985.msg33251.html#msg33251
. In the course of that thread, I was trying to make doughs that would last for many days. I wasn't expecting to see spots in the doughs but once I started to observe them, that got my attention and I proceeded to conduct a wide variety of experiments to see if I could determine the cause or causes of the phenomenon. You can read a summary of those experiments at Reply 78 at http://www.pizzamaking.com/forum/index.php/topic,3985.msg41385.html#msg41385
. As you can see from that post, I largely blamed the flour for the spotting, specifically, the high-gluten flour that I was using. Also, I saw that the spotting tended to appear after several days of cold fermentation although in one case I saw the spots after 2-3 days.
More recently, Walter (waltertore), in a post earlier in this thread, at Reply 13 at http://www.pizzamaking.com/forum/index.php/topic,27729.msg280731/topicseen.html#msg280731
, made the observation that got my attention that "long fermentations that started with cold water make for a more spotty dough". That was not something I had considered or tested before as a possible cause of spotting even though the doughs that I was making did make use of cold water. That was by design. I used the cold water to achieve low finished dough temperatures, along with the late addition of IDY, the use of metal storage containers, and short dough preparation times (usually about 10-12 minutes) with gentle kneading to keep the heat of friction down, all in order to extend the useful lives of the doughs to many days. It's possible that the spotting I observed at the time of my tests had something to do with the water temperature, not the type of flour.
As you know, spotting of the dough is harmless, whatever its causes. But, like you, I like to understand the causes, if only to tie up loose ends or to satisfy my curiosity.