There is a litany of things that can cause the "Smoke On The Water" syndrome, besides too much Deep Purple. If you have an unmodded game, the main problem causer is "shelling-out" to Windows. In other words, you <Alt><Tab> or some other keypress and go to the desktop to consult your detailed map of the harbor, then go back in to the game. Not good. The game is an old single-core, exclusive process, 32-bit app, and has a "hook" into certain aspects of Windows, such as the audio stream or the video stream, which gets changed when you shell-out. You might notice that night and day no longer match the clock, or that your crew is suffocating for an unusual build-up of carbon-dioxide in the surfaced sub, etc etc. Save the game, exit the game. Re-start the game, and reload the scenario. Hopefully that "fixes" it. (my suspicion)
Another of the biggies is not activating the mod properly. If you have a clean install of SH4, run JSGME and let it make the MODS folder. Then run the "Tasks - Generate snapshot of game files", which will help you when you go to change mods later. Then make sure the Save folder for the game is emptied. It defaults to "C:\Users \UserName \Documents \SH4". Delete the "SH4" folder and everything under it. Activate the mod. Run the game. It will create a new SH4 folder for you. You will have to re-set your screen resolution and other gameplay settings.
