Hello E.,
Maybe I can shed a little light on what you are noticing. I work for a dairy cooperative, and we make whey protein concentrate for baby food and baby formula companies. I am a new employee so I will give you my small amount of simplified knowledge.
When you make cheese, you have a milky subtsance left over that is "whey" (like Little Miss Muffet's gig). The whey is then sent through huge dryers, and made into a powder. This process produces many different products, depending on what you are attempting to use the "cheese by-product" for.
If you make a product called Whey Permeate, you get a very low nutritional content powder that is used for things like cookies, chocolates, or confectionary items. It is more of a sweetener than anything.
If you pull out the protein from the substance, you get a whey protein concentrate (WPC). Generally, you can make a powder that is between 78% - 90% protein. This product is used in nutritional items, body building foods and supplements, geriatric nutrition, and there is a huge market for baby food and formula that uses WPC.
If you ever compare formula brands you will notice a vast difference in colors and textures. Most of this is due to the fact that different cheeses make different colors...An orange cheddar is going to give you a much darker powder than one from a white cheddar. Another difference you may note is the flecks you are speaking of. I would venture to guess that you are noting "scorch particles."
As the whey is dried at a very high rate/temp, it can sometimes bake, and in essence "burn a minute amount of the powder." It poses no health concern or problem, it just cannot be eradicated from the whey protein as it is so extremely small. It sometimes is a natural occurrence, and sometimes it is because the company making the product baked it at too high of a temp or another issue during the drying process. You can compare it to making candy and the way you "carmelize" milk based products if you cook them too fast or too hot.
I would like to assure you that the customers that purchase whey protein for baby formaula have the ABSOLUTE STRICTEST product regulations. They not only require companies selling the product to test every single bag of product and provide these results, they also do all the tests over, themselves, and with outside labs before allowing a single bag into their facility. Baby food and formula customers are the absolute nightmare of the industry (as well they should be). Their requirements, testing, analysis, and documentation is excruciatingly exact, and only the highest grade products are used in the U.S. If you ever tour a facility that produces baby formula, it is like entering a miltary zone where you wear clothing like space suits, and the measures that they take to secure their product and it's safety are mind boggling. Unfortunely, in some foreign countries they are not so discrimintaing, and you find issues like the melamine incident happening.
It is great that you are being thorough in reviewing what is best for your children. Honestly, after working in the industry, I feel more comfortable, now, with baby formula than I did before. I would have no qualms about Parent Choice as it is what I gave my second child.