The strange thing is, that sometimes it is possible to save and load in port or even submerged. I have had this experience too.
Try to start the game without SH3 Commander, double click on sh3.exe and you will probably be able to load the last saved game.
If the above did not solve your problem, as said before load a previous saved game ... or as the GWX manual said: rename (or copy the folder) your Kaleun (career) for example Hans Balz to Hans Balz
x (see the
x).