This actually happens to me too. I use the auto-targetting system and sometimes, when I pop the periscope up it's like the game doesn't recognize there is a ship there to target. No little triangle pops up when the crosshairs are on the ship, I can't lock onto it, etc. Which means I can't fire my torps at it, unless I feel like firing blindly with no firing solution. Sometimes it randomly starts working after a few seconds (or at most a couple minutes), sometimes it does not. In the cases where it doesn't I usually just raise/lower the scope a couple times and it starts working.
I have also noticed that when I can't target using the periscope I also can't target using the on deck binoculars, I've surfaced a couple times when this has happened to check it out. I have checked to make sure I didn't leave my crew at battle stations too long and caused them to be really fatigued or even asleep, as I have experienced that before and it's basically the same symptoms, the crew is so tired they don't detect the ship is there even though I can clearly see it in the periscope.
This problem started happening for me when I uninstalled the +25% torpedo power mod and installed the real sinking mechanics mod, and these are the only mods I have ever used. I'm not saying either of these mods caused the problem, but it's possible some game files were corrupted in the process of installing/uninstalling the mods. Or it may be a bug with the new mod, but a lot of people use it and it's likely it would have been caught by now if that was the case. It's really more of an annoyance than anything, and like I said it usually goes away by itself. It's certainly not worth the 4-5 hours it would take to reinstall the game, to me anyways.
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