The bug that allows enemy units to detect your sub using their air search radar still exists after 1.3. This has the effect of allowing japanese ships to home in on your sub way before they had surface radar historically. Play the photo recon quick mission (1943) to see this at work.
See:
http://www.subsim.com/radioroom/showthread.php?t=113010
http://www.subsim.com/radioroom/showthread.php?t=112994
Changing the max range value of type 13 radar to 1 (in the AI_Sensors file) solves the problem. You need the minitweaker to change this type of file.