Fearless
I can't explain the strange behaviour of your torpedoes, but like you I use auto targeting. Trying to figure out all the parameters needed for a manual solution is just too much hassle, I'm not as "hard core" as some others. Let me give you my understanding of how it all works and my experience with SH4.
The only time I really use the PK is when I'm manoeuvering submerged to get into position. What it does is that it gives me a real time "update" on the target's course, bearing and position relative to me via the attack map. However the information remains valid only if the ship does not change course or speed, so every once in a while I pop my scope up, find the target, turn off then turn on the PK again to refresh the data and update the firing solution.
The only situation when the PK has screwed up my firing solution is when I forget to turn it off before firing. You may know this already, but if the PK is left on then all the data the TDC needs to generate the firing solution is taken from the PK. Your scope could be pointing to a different ship or even 180 deg around but it makes no difference. If the target has not altered course or speed then there shouldn't be any problems, but there are times, like firing on a second ship, when I find my torps are headed for the 1st target and then I realise that the PK is still on

.
Now, if the PK is turned off, the TDC gets its information from wherever your scope is pointed and continously updates the firing solution. That's how I spread my shots along the length of the ship. If the target is locked, then all shots will be aimed at the centre where the triangle is. In other words locking the target forces the scope to be locked in position relative to the centre of the ship, hence all firing soultions generated will be for shots hitting the centre of the ship.
Hope this is of some help.