Sewbeadit,
I can't speak to all the pre-cuts at LQS-es, but I did buy some pre-cut batiks at JAF & those ones seemed identical to the bolts. One of the many reasons I've become a quilt-shop snob & only shop at JAF for batting & notions. I even had a spool of red thread from a big box (don't remember which) that ran and faded when washed. What a mess!
I never remember the brand of batiks they carry at my favorite LQS, but those ones don't run regardless of whether they are pre-cuts or off the bolt. I always worry a bit anyways & wash them separately from the rest of my fabrics first, but then the second time I usually toss them in with everything else along with a color catcher and I'm good (unless, of course, it is a red or a deep purple & then I'm not brave enough yet).