There is a mod called Transparent Konsole- makes the torp loading screen clear. After loading this it fixed my problem, I had the same thing happen to me.
I also found that only loading 2 fish at any one time keeps it from happening. It's when you move 3 or more, or queue 3 or more that it becomes a problem.
And yes, when it happens the torps do go "missing".
I'll see if I can find the link.
http://mpgweb.de/downloads/index.php?act=view&id=574
Use that and move 2 at a time and your set. Easy to install, just one file and no editing.