MM has it. Mods will not "take" properly with the path to the game involving a Program Files folder. You are in "C:\Program Files (x86) \Steam \SteamApps \common \Silent Hunter 4 Wolves of the Pacific", and while it might look like that mod(s) took, only the graphics files were kept. Anything with "*.ini" or "*.cfg" especially, were rolled-back by the wonderful Windows 'security' features in UAC and other "technologies". Newer games do fine, but just about anything that is DirectX v9.0c based will have trouble, and SH4 and JSGME do. Refer to
Moving a Steam Installation and Games if you have to move SH4. If you have a valid 2nd hard drive, you can put another Steam Library folder on it, such as "D:\Games \Steam \Silent Hunter Wolves of the Pacific" or whatever you want to call it, and you will not have the issue of bad mod activations. 2nd of all, which Seawolf mod do you have installed? JHapprich's? You want to make certain the mod you are using is made for v1.5 of the game, if that's what you are using.