I am not sure what to think of that - but you're getting it on a 2nd copy of the game... strange. Sorry about the ensuing verbosity, but there can be a few things to check...
So you have Windows 10 x64. Do you know what your video card is? Your display monitor and its "native" resolution? Windows will list that as "... (recommended)" on its settings screen. You should match the video stream from the "native" of the monitor, to the Windows display settings, and in the game's "Options" "Graphic Settings". You might also have to noodle with the SH4.exe "Properties" settings. Navigate into the game folder, find the SH4.exe file, right-click on it, and choose "Properties" at the bottom of that list. The image below is the way I set one of my computers:
the smaller "Sh4.exe Properties" window is from clicking on the "Change high DPI settings" button. One one of my computers, I had to use the "Program DPI" at the top of that little window, and have Windows set to "Use the DPI that's set..." "when I open this program". For whatever reason, that computer's video card wants to use Win10's "smoothing", which ~really~ messes with the display. Dependent upon your display, you might have to use "Disable fullscreen optimizations", or maybe not. In almost all cases though, you will have to alter the "high DPI" settings.
One of the biggest issues SH4 (and 3) has with the 'modern' Windows OS, is UAC and other schemes used to protect the users from themselves. The old DirectX v9 games are built to the Windows XP paradigm. With Vista, the "Program Files" folders became "protected" by windows. As such, a program has to be properly "authorized" by Windows to allow alterations inside of the folder. JSGME.exe is a WinXP app also, and is not recognized by Vista or Win10 as "authorized", so anything you do with it that alters what Windows considers as "system" files, such as *.ini and *.cfg files, will be "rolled back" quicker than prices used to be at Wally World. If SH4 on your computer is installed in a "Program Files" folder, your mod activation most likely is not complete. On a 64-bit computer, the SH4 Installer will default to using "C:\Program Files (x86)\...". With Steam, you have to use
Moving a Steam Installation and Games, and it can be a bother, mostly done to comply with Steam's "licensing". With the disk install you have, you can copy the "Silent Hunter Wolves of the Pacific" folder, and paste that into a folder of your own creation, such as a "C:\Games" folder. After that, you will have to either clear the "C:\Users \UserName \Documents \SH4" folder (or similar - OS configuration dependent), or use
MultiSH4 and create a new Save folder to point that copy of the game to, which segregates the Save information. You will also have to make a new shortcut to that SH4 file...