My knowledge of shell scripting has nearly run out. But there must be *something* in the big script that is affecting yafu. Have you done anything with stdin or stdout in the big script? Try adding </dev/null to the yafu call. And look for anything else that could affect yafu. You could try cutting a copy of the big script down by deleting bits of it until yafu works (hopefully before it's the same as the small script!)
Sorry I've run out of ideas.
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