Hi Robert,
I don't know whether I can be much help, and forgive me if I stating pretty basic stuff here. The simple fact is that the mod enabler, which I use in several other games as well as SH3, never gives me any trouble at all.
The only time I have problems is because of 'user error'. Following that theory, check out the add-on folders in the mod folder itself to enusre that you have the correct locations for each - sometimes, especially when using installers, a 'parent' folder is installed containing the mod, and obviously this means that the sub folders will not be installed in the correct location. This still happens to me sometimes if I'm not careful.
I have never seen duplicate folders in the root. The enabler creates backups of the replaced files in every case, but these should be within the target folder for each particular mod.
Hope this helps.
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