Just discovered a good article by Sam Ng of UX Matters who gives us the benefit of years of user testing experience particularly around card-sorting: Card sorting: mistakes made and lessons learnt.
I’ve found the same experience. For example,
I’ve accepted the fact that card sort analysis—much like usability test analysis—is often messy and subjective. It’s part science, but mostly art. As with many aspects of our work, there isn’t necessarily a single correct, quantitative answer, but rather a number of different qualitative answers—all of which could be correct. Our job is to use our experience and our understanding of people to make judgment calls.