I had the same problem when I started manual firing, until I realized I was forgetting the last "Check" on the notepad (after you've checked each individual measure into it)
Also, preparing shots in advance, rather than taking measures while locked and firing, helps a lot in solving that problem.
If not (this is what used to do before I realized about the above written), just go to the TDC after the info it's been entered, and add a couple of knots to the target's speed. Yeah yeah, not the most proffesional way to do it, but hey! A sunk ship is a sunk ship, regardless of how you managed to get it