A couple minor problems I've had with the new stockpiles:
In my latest fortress, world generated with the current version, dwarfs won't move or use dwarven syrup. I tried building a food stockpile that accepted nothing but dwarven syrup, but they wouldn't touch it. I tried building a huge stockpile set to accept all food, and still the dwarven syrup was ignored. They won't cook with it either, but I assume that is because it isn't in a food stockpile. I didn't notice the problem until I moved my food processing area, when I demolished the farmer's workshop the barrels of syrup were left behind, and there they sit to this day. I tried making a barrel of syrup in my new farming workshop, it also got left in the shop, with no tasks assigned to it.
The other problem involved furniture stockpiles and jewelers. I didn't want bins or bags encrusted with jewels, so I set up a furniture stockpile near the jeweler's workshop and forbade bins and containers. This seemed to fill up and work well, until I told the jeweler to encrust furniture. He walked right past the stockpile to get to one quite a distance away, and then started carrying a bag of sand back to his shop. D'oh. It was like forbidding some kinds of furniture caused him to not see it as a real furniture stockpile at all.
I made a second furniture stockpile, this time I left all types of furniture allowed, but in the materials menu forbade wood, silk leather and cloth to exclude bins and bags without specifically forbidding them (of course, this also excludes wooden beds). This worked fine. The jeweler happily encrusts furniture from a furniture stockpile that has some materials forbidden, as long as no types are forbidden. I can make do without fancy beds so it isn't a huge problem, but it does seem odd.