I just finished unpacking and punching my DR-PotF (as well as other things, but I'm really only miffed with the quality of PotF) and I'm not impressed with how the cuts lined up.

Most of the spiky things that go on the fortress walls are off-center.
Most of the grated walls/floors are off center and in many cases the holes are deformed, don't line up even with each other or weren't punched through the whole way and I needed to cut them myself. And there's this one glaring instance of a door texture still partially visible on the outline of a doorway.

And finally the furniture doesn't want to hold together at all. Will need to glue things together, even the elements that were supposed to be re-configurable. Which defeats their purpose I'd say...

Did I just get a really bad box or something?

Sounds like it. I got a few boxes - most were spot on cut-wise, but one was somewhat off. Not S bad as you described, but enough to notice up close. From the table top level I doubt I'll notice.