I’ve just returned from some surgery in hospital (and slowly recovering) so sorry for the delay in responding to your post.
I ran 1.04 million objects * 4 variables through the non-hierarchical routine into 14 groups ok with random data and reproduced your error in the box and whisker plots. We had improved the precision in some areas in 3.04 but this one has slipped by. So, we will need to work on it!
In the meanwhile (sorry), export the data table (it has the data and the group identifiers) to any stats pack (eg Statistica).