Can't be OTC because it doesn't touch any environmental aspects (I'm using it, as well). ISP I'm not familiar with (it's a mod that popped up when I was away from the game), but I think it only deals with how the sub interacts with the water. The periscope zoom in/out issue I'm getting, as well; it takes a few tries and a bit of clicking to get it working but it's only a minor issue so I mostly ignore it.
When I set about merging ISE with TMO I did notice that the enemy's sensors had been affected, but I have tampered with their detection range in my game so I had to readjust their sensors to bring them to my liking again. Play for a while and see how the enemy behaves.
ETA: OK, I poked inside ISP and I see that it comes with its own version of scene.dat. Try this: deactivate ISE #1 New clouds+Waves and then ISP, remove the scene.dat file from ISPs Data folder and activate it again (do not reactivate ISE #1). If the water is back to normal, you've found your culprit (and hopefully didn't mess up the mod too badly!).
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Last edited by DrBeast; 07-10-15 at 03:06 PM.
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