Try using the MarkerFaceColor property.
Example:
x = 0:pi/32:2*pi;
y = sin(x);
z = cos(x);
plot(x,y,'s',x,z,'-','MarkerFaceColor',[0 0 0])
That seems to work fine, since your second set of data is plotted with a line marker, but you could always also split them up into separate plot commands if you for some reason wanted to control the marker face color of each.
