One source of error is the head-on angle of your boat. The game considers the aspect of the target to the seeker head, so a head-on boat has a smaller lock-on target than a beam-on boat. Due to the nature of trigonometry and the angles involved in this problem, if the torpedo is off by just a few degrees in its approach (compass-wise or depth-wise), your boat will look much bigger from the head on approach due to now seeing some of the side or top/bottom of the boat. However, if you do this test from a beam-on perspective, any error in approach angle will be much more forgiving. (To verify, just try looking at some narrow object in real life from the side and from the front and adjust its angle to you a little bit each way to show the effect). However, we're talking no more than maybe a 10% difference here. Obviously, your numbers are much more different than that.
Have you tried the test without the layer? That's just introducing another variable here (that you are correct in thinking shouldn't matter with how you've done the test). I would try without the layer and see what happens.
Also, just to double check, you did these tests at the same layer depth? Layer depth always changes each time you reload a mission.
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