A Matrix Object set to Thinking Particles is already making particles so you just need to add a Particle Geometry object and put in an Xpresso tag with a PPass node that passes to a PShape node which links to your sphere. It won't render correctly unless you start at the beginning. In my quick test here it leaves stray particles at various points and I don't see any difference between the motion of a sphere in a Cloner set to Object or the Matrix set to Object but my quick Metaball may not be complex enough to replicate your problems. ...Or I'm missing something obvious...
342_clonervsmatrix.zip
