Recently, a question was asked about the spatial join tool, and its failure to calculate the desired data.
I ran into the same problem, but none of the solutions that were offered there solved it.
- I ran the tool as a standalone process, and it worked fine
- I made sure both my layers (a polygon and a point) are the same CRS, still failed
- downgrading is not an option
Running 64bit standalone 2.12.1 Lyon on Windows 7