Consider something like
figure plot(sin(0:0.01:pi)) axis tight set(gca,'box','on','ticklength',[0.02 0.05])
then export the graph to PDF or whatever. The lines of the graph are on top of the tick labels and the axes. (Furthermore, the lines of the axes don't meet correctly, but that's another story.)
Is there a way (that can be automated) to have the axes drawn on top?