I don't play SHIII so I feel almost as if I oughtn't to be posting here, but shooting is shooting after all. I can't comment on the actual interface controls, but if you enter all the target data [range; speed; AoB] and the torpedo goes straight ahead when fired, then it sounds like somehow, the target data isn't getting to the torpedo. If I find the thread I'll edit the link in, but I saw recently on the SHIV forum a table of speed offsets for leading a target when using zero gyro angle shots. Should work for you in SHIII because the physics doesn't change. How about loading up the torpedo training mission and playing around with the controls so's you know that they're all working as they should? Maybe enter a speed of ten knots for a stationary target and then aim off to hit it, or practice firing with extreme gyro angles - After all, when circumstances compel you to shoot at a 90 degree gyro angle [which they will, eventually] you don't want that time to be your first.
A couple of techniques that are worth your time are RR's Fast 90 and the Vector analysis method. The latter one will work with any sim and I can't see the former not working in SHIII.
If all of this is already known to you then I apologise for taking your time. it sounds to me like you may be making a simple mistake somewhere, that you'll kick yourself for when you spot it. Something I do pretty frequently
Good hunting.....
P.S., until you work it out, try saving the game before shooting - then you can go back and look for the reasons why you missed - assuming that's what happens....