I am using a focused mask and signal subtracted particle images.
Ah, this might be the issue. Have you tried using non-subtracted particles? The way in which we apply the focus mask effectively does signal subtraction as part of the classification (see this thread or the 3D classification tutorial).
Note that we changed the way we handle masks in CryoSPARC v4, not v4.1 – so this would not explain why you see different results between v4.1 and v4.0.2. Perhaps the signal subtraction is interplaying with the pre-multiplication bug in some weird way in v4.0.2.