Edges of scatter plot don't respect layers

When using scatter plot, e.g.:

scatter(X,Y,17,CUSTOMCOLORMAP,'filled','MarkerEdgeColor',[0 0 0],'marker','o','linewidth',0.1);

I generally end up with situation B (undesired), in which edges don't respect the layer structure. I was able to get the A plot by setting:

opengl software

Unfortunatly, after running some completed unreleated code, this trick doesn't work anymore (even after restarting Matlab). I also tried unsuccessfully:

opengl hardware
%or
opengl hardwarebasics

What am I missing?

I have this problem both with R2018a and R2018b on different machines both running on windows 10 and with intel HD graphics cards.

Thx

[Star Strider]

What MATLAB version (release) are your using?

[Daniele Mascali]

MATLAB Version: 9.5.0.944444 (R2018b)