I'm not sure what is going wrong here. It works in some projects, but not in others. I can't figure out what the difference is between them. To test the problem, I created a point set with a single point at a position I am sure is inside the cube. When I call IndexAtPosition, I sometimes get obviously wrong answers. For example, I sometimes get inline or crossline indexes that are negative or way beyond the maximum index. The z-dimension index also comes back with a very unrealistic answer too.
I am fairly certain that my data is all consistent, i.e. same domain and CRS. There must be some settings I'm not checking.
Unfortunately, I made a mistake. One of my data points was in fact outside of the cube area when the cube was rotated.