There are several things to remember about this game. One would be that as good of a game as it is, it is NOT perfect by any stretch of the imagination. A big thing along those lines is the sad fact that nowhere in the game's documentation do they warn at all about what to do if you mod the game, apparently assuming that you would never do that, since their configuration of the game is so near-perfect. They also could not project what would happen with a Windows XP 32-bit, DirectX v9.0c game when it came to the 'modern' Windows OS and 64-bits, with UAC and other "technologies", so there is no documentation from them on that aspect of the game either.
First thing, the game does NOT like it if you "shell-out" to Windows, which can be minimized under certain conditions, and on some computers. The more hardware (cpu, ram, hd space, etc) you can throw at it, and apparently by pausing the game prior to using the Windows key to shell-out. There are still certain activities that will cause the game to "get lost" in its own address space. When the game does odd things after shelling-out, the game can often be restored to an OK condition by Saving the game, exiting the game, re-starting the game, and then Load the Save and continue. Usually.
Second, if you previously had a mod applied, and then are now doing Stock while trouble-shooting issues, but you did not empty the Save folder, then the game is still attempting to run with the old data from the game's previous state of having the mod(s). Try to clear the "C:\Users \UserName \Documents \SH4" folder (or use a Windows Explorer short-cut to it). Try the game again, and see if it doesn't restore some semblence of normalcy. Just know that all of your previous sound, screen, and game settings will have to be re-set. Even if you haven't modded the game, it might help to try clearing the Save data anyway, to see if that helps in these situations for you. v1.5 of the game though, is the "Gold" standard...
sorry, bad pun...