I do not know the reason for the problem at the moment.
I would, however, suggest that it is typically better to create the line objects before a loop, and then update the line objects within the loop, instead of calling plot() each time.
L1 = plot(app.UIAxes, nan,nan);
L2 = plot(app.UIAxes, nan, nan, '.g');
for i = 1 : n
%stuff
L1.XData = A; L1.YData = B;
L2.XData = x1; L2.YData = x2;
drawnow();
pause(0.5);
end
