The problem is not TMO, but rather, Windows itself. Microsoft added User Access Control (UAC) to Windows with their Vista release, in an effort to protect the computer from the user and from malware. It's what pops up those little message boxes for 'Do you wish to let this application access your computer' and others of that ilk. Part of the UAC schema also included "Protected folders", which includes the Windows folder and all of its sub-folders, and the Program Files and all of its sub-folders. Nothing is allowed to be changed in those folders unless it is changed through a Windows utility, such as InstallShield or similar. So, when you activate a mod, and then go to run the application (SH4 in this case), Windows 'notices' that the files have changed, and puts ~SOME~ of the originals back from a repository. To change this behavior, you'll have to move your install.
De-activate your mods with JSGME. Downloaded SH4 games such as from Steam sometimes have another layer of "protection" of the Steam license, which prevents direct copying, but as of the last time I moved an application from Amazon, they wrote to the registry for their license, and didn't care about the path to the executable, so what you could try first, is to select the Ubisoft folder in the Program Files (x86) folder on your computer, press the <Ctrl> button, and while holding it down, press the <C> key. That will "copy" the folder and everything below it. Now go out to the C:\ root, or any other drive that you have available that can hold over 4gig of data, and press <Ctrl><V> to paste the folder there. It will take a while for the files and folders to copy over, but when it's finished, you should be able to enable a mod, and have it "stick". The other thing(s) you'll have to change are your shortcuts for SH4. Either build new ones, or edit the ones you already have to point to the new location.
Let us know how you get along, which ever way it goes...
