I am totaly satisfied with everything about my bagels - flavor, texture, etc. - except for the dark splotches which are actually bubbles on the surface:

This does NOT appear to be a function of external factors such as uneven heat distribution or cooking temperature or rack location - I've messed with all that with no success. My guess is that is has to do with the way the dough is fermented or proofed. I use only wild starter, and among the ingredients are barley malt syrup and dried milk. After kneading, the bagels go into the fridge to retard overnight and then proofed at room temp for about an hour. Then boiled for 30 seconds, baked for 20 minutes. Perfect in every way except these ugly splotches.

Any suggestions would be greatly appreciated.