So it is probably happening because subplot deletes a plot when it is overlapping with the previous plot. I suspect that happens because of conflicting positions values between the subplot tile number (i.e. subplot(2,1,1) etc) that has its own default position, and the position you entered.
So instead of using subplot(m,l,p, 'position', [ a b c d])
, you can solve this issue by using subplot
just with the position info as follows:
subplot('position', [0.1, 0.4, 0.85, 0.45])
plot(1:10);
subplot('position', [0.1, 0.1, 0.85, 0.15])
plot(1:10);