3D classification - unreproducible results with the newest version

Another quick clarification: are you supplying your own solvent mask? If not, you can try supplying one along with the focus mask.

The solvent mask should be a soft mask that covers the entire target – the mask output from an upstream refinement job should typically work well. There was a recent bug pointed out in v4.1.1 that affects automatic solvent-mask generation when a focus mask is supplied.