People are often confused about Kona. Kona is the copyrighted name of a type of fabric produced by Kaufman, the manufacturer. Kaufman Kona is the same everywhere. However, there is another fabric manufacturer that has the name Kona Bay. Sometimes people see Kona Bay on the bolt and think it's Kona cotton. Well, in a way it is; however, it isn't Kaufman Kona!
I have seen arguments both ways about whether the same line of fabric comes in different qualities. I honestly don't know for sure. What I have noticed, however, is that sometimes fabrics at Walmart (and less frequently at JoAnn's) are slightly misprinted. Printed fabrics run through rollers with different colors and, if the positioning is slightly off, the colors will be slightly off. This makes the print more "muddy" in appearance. If you're not used to looking for this, it's easy to miss. If I am buying printed fabric at a non-LQS, I tend to take a close look at the print to make sure that the colors are clear and the lines defining the print are sharp.
I do think that flat folds are often "seconds". I have found that flat folds are often not as pretty as other fabrics.