There can be a difference in grade of the fabrics between the LQS and the chains. There are several runs made of fabrics and the quality can vary.
However, I just learned from a LA teacher/dealer in a LA class that the Kona Cotton Solids are exactly the same product in both types of stores.
Here is a link to an article and see the last paragraph:
http://ezinearticles.com/?What-Makes...ic?&id=2225860