Have you extracted them according to the readme files? It's easy to right click - extract to <folder> then copy that folder into the MODS folder and what you get is a double folder effect, where the mod is in a folder in the folder you just created. When you install it, it doesn't overwrite any files as they all go to the wrong place.
Best way to check is in the MODS folder, the TMO folder should have a data folder in it, if it doesn't and has another folder called TMO in it, then it's been extracted and a double folder created.
Boy, that sounds confusing, but it's hard to explain clearly. For me anyway.
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