Since you already use a clearing bath after bleaching, I would say that MnO2 is the least likely source of your problems, and I would only look into that once you have excluded all other options. If you are not sure about your clearing bath, there is a thread here on APUG where a "rinse with dilute sodium metabisulfite (a 3% solution does the trick)" is suggested. Key seems to be Sulfite ion in acidic environment.
Neither Ag2S, nor tiny Silver crystals will be affected by fixing, so I suggest you fix your milky test clips and check whether brown stain is visible and then check for Ag2S vs. tiny Silver Crystals. Tiny Silver crystals can be bleached away with C41/E6 bleach, while Silver Sulfide will be unaffected.
Rudeofus. Thank-you for the very clear answer and methodological approach to investigating the problem. That's just what I needed!