If you dont see an obvious difference it aint installed right.
Make sure that you dident nest the mod folder into another folder that you created.
Typically the unzipping of a large mod like TMO will have everything neatly packaged into a single folder with several subfolders under that.
So dont have an empty folder with the mod folder inside of it
x:/programfiles/ubisoft/SH4/Mods/TMOmod/TMOmod should be
x:/programfiles/ubisoft/SH4/Mods/TMOmod
Hope thats kinda sorta clear.
Oh yea dont forget to remove it with jsgme before trying to put it back in again