I don't know about other manufacturers, but I've written to RK (as have other members here) and they state that they apply the same rigorous selection process to all their fabrics, regardless of destination. They do not have different standards for quality for big box stores vs. LQS'es.
I personally often shop at LQS'es because they have a much wider selection of RK fabrics, but I've bought at both places... used RK fabrics from JAF, online and my LQS together in the same quilt and cannot tell the difference. One thing that I have found a bit problematic at JAF is that often the bolts are very sloppily wound, so I have to spend extra time & money squaring the fabric up before I begin. Sometimes if I point this out, the lady at the JAF cutting counter will cut me a bit extra at no charge (sometimes not).
There are occasions when there are issues with the fabric regardless of which vendor received it. I have a JAF Superstore and 4 LQS'es nearby. At one of the LQS'es (with the widest selection of Kona solids), I once found a fabric that was of unacceptable quality on the shelf. They immediately removed it from their inventory & received a replacement from RK. I found a couple prints at JAF over the years by RK that has issues. They just put them back on the shelf. I suspect, but don't actually know, that may be why it seems to some that there are different "runs" of fabric for JAF. Perhaps it's just that the LQS'es are more conscientious about inspecting & caring for their stock.
If you can get a good deal on Kona at JAF, go for it! Even if you have to lose a bit more fabric squaring it up, it's usually still a lot cheaper than buying properly wound fabric at the LQS. With solids, do buy as much of each color as you would need (maybe plus a little bit for oopsies) because different dye lots can cause slight variations in the color.