First of all, "Welcome to SubSim Suzuro!"
2nd of all, where do you have the game installed? If you used the "default" installation path that the installer uses, then that would most likely be the problem. The "Program Files" folders are 'protected' Windows System folders, and as such, 'un-authorized' changes are not allowed. Since both Silent Hunter and JSGME were written prior to the use of User Access Control (UAC) in Windows Vista and later, they were not written to that Windows spec, and are therefore not on the 'authorized' list. When you activate a mod on the game inside one of those folders, Windows "sees" the changes, and will roll them back to 'protect' the system.
Depending upon your game version, you might be able to just make a copy of the game folder and then paste it into a new location, such that you make a new "C:\Games" folder, go into "C:\Program Files (x86) \Ubisoft" and copy the "Silent Hunter..." folder, and then paste it in the "Games" folder, you will then be able to apply mods. You will have to create new shortcuts for the game though. Or you could un-install what you have, and then delete the "C:\Users \UserName \Documents \SH4" folder, which is the game's 'Save' folder. Then re-install the game. When it comes up and asks where you want to install the game to, change the install path, either by clicking on the folders and browse around, or by inserting the cursor in the path they show, and removing that "Program Files (x86)\" part, or whatever you want to name your install folder. If you have the Steam version, then refer to "
Moving a Steam Installation and Games". The method you use depends upon your computer configuration.
Another problem can arise when applying mods in that if a player does not empty the "Save" folder mentioned above (generally "C:\Users \Username \Doucments \SH4"), the game will not re-create the folder, and since the game does not over-write existing files, it will often not make a whit of difference when you go to run the game after activating a mod, other than you might have a half-modded, and half-unmodded cross-breed that doesn't work correctly.
A last thing (for now) that can muddle an SH4 install, is failing to install the DirectX v9.0c files and the codecs when that choice comes up - but that prevents the game from getting beyond the menu. If your game ran fine prior to trying to activate TMO, then you should be good to go in that regard. Let us know how you make out with it, or if you have other questions!
