For vamac53, you might want to read CapnScurvy's thread
Windows10; Large Address Aware; SH4 Install. It gets rather involved, but the addition of using LAA makes a world of difference in game stability, and CapnScurvy walks through his SH4 install. IRISH4Life could probably benefit from a read of it too, though implementation on Windows 7 is a bit different.
The main thing that causes issues is Windows. SH4 was written back in the wonderful Windows XP days. As such, there really wasn't a lot of "security", and most everything on the computer could be edited. Microsoft decided to "protect" the user from rogue invaders (who??), and with the release of Vista, we had User Access Control (UAC) and "protected" folders. Windows tracks all edits in folders such as "Program Files" and if an unauthorized change is made, the files are rolled back to their previous state. JSGME is not "authorized" by Windows to make changes, so mods get rolled back. You'll see some files "stick", like the pictures or movies, but none of the CFG files remain.
The best thing to do is to install any older games in a folder of your own choosing, making a path like "D:\Games \Silent Hunter..." or "D:\Ubisoft \Silent Hunter...", etc. is highly recommended. CapnScurvy gets into that in his thread. Now, Windows 10 throws in some other issues, including Update problems (imagine that...). THEBERBSTER has info on those issues somewhere on SuibSim, but I can't find them right now...