When you say straight from the box, which box?
Are you playing Silent Hunter 4 V1.0 or are you playing Silent Hunter 4 Gold Edition, this has the U Boat mission addition as well as patch V1.5
If you're playing just SH4 V1.0 you MUST patch it to V 1.4, can do this at the UBI website. It's a free download.
Auto targeting is just that. As Torpx said just lock the target, open the doors and pull the trigger when you get a green arrow in the scope.
The L key should lock and unlock a target also the red button on the torpedo selection panel should do the same.
From what you are describing it sounds like you're not patch to at least V1.4 and all kinds of strange things can happen.
Magic
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Reported lost 11 Feb. 1942
Signature by depthtok33l
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