Hello,
Can you try FXAA? FXAA is post-rendering, thus it can mitigate certain aliasing caused by some shaders MSAA is unable to handle. Maybe such shaders are involved in the case of the cubes 2-6. Either this or change the pink rectangles pipeline to that of the green one. BTW, why do you need vtkGlyph3DMapper instead of a common polydata mapper?
take care,
PC