I have matrices x1, x2, ...
containing variable number of row vectors.
I do successive plots
figure
hold all % or hold on
plot(x1\'
Starting from R2014b there's a simple way to restart your color order.
Insert this line every time you need to reset the color order.
set(gca,'ColorOrderIndex',1)
or
ax = gca;
ax.ColorOrderIndex = 1;
see: http://au.mathworks.com/help/matlab/graphics_transition/why-are-plot-lines-different-colors.html