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Actually this problem cannot be solved without an extensive redesign of the sorting feature.
You are not supposed to use %fn like this: it should be used in a filename context, not a folder context.
Also, I don't understand the need, why would you want to have the original file name as a folder name?
So when you have the NZB name "My Show S1E1" containing the file "My Show - S1E1 - First one.avi",
you would end up with this: "\path\TV\My Show\My Show - S1E1 - First one\My Show - S1E1 - First one.avi".
Isn't it better to use "%sn/%fn.%ext" ? This would give:
\path\TV\My Show\My Show - S1E1 - First one.avi
Or "%sn/Season %s/%fn.%ext" giving:
\path\TV\My Show\Season 1\My Show - S1E1 - First one.avi