I just took another data set in the Samples folder, Fitness, and performed a two-way clustering using only default settings and changing nothing:
![Capture.PNG Capture.PNG](https://community.jmp.com/t5/image/serverpage/image-id/18538i1435E5254F679030/image-size/large?v=v2&px=999)
My guess is that you have some column properties or row states for color that are interfering with the default coloring.