Here is a short sample that shows the behavior:

graphics_toolkit('fltk');
close all;

figure(1);
plot(1:10);
legend('legend A');
title({'line 1','line 2'});

figure(2);
subplot(2,1,1);
plot(1:10);
legend('legend B'); % will be misplaced
title({'line 1','line 2'});


subplot(2,1,2);
plot(1:10);
legend('legend C');
title({'line 1','line 2'});

With the fltk plotting frontend the "Legend B" will be displaced by a lot, compared to the other two legends. I would say it's placed wrong. This happens on Linux as well as on Windows (MXE).

Addidtionally "legend A" also seems to be a bit off the right position.

With gnuplot as well as with Matlab all three legends are positioned in a similar manner inside the box, and look fine to me.

If you make the title a one line object, then it looks much better. Then, only legend B (in the subplot) is off position.

Also the order of calling "title" and "legend" seems to be important. If you swap those function calls, the result looks totally fine.