I had this issue too. You must have all the modules as well in the correct place. Those being the DLLs. How to find them? Look on that iso site for "ctr_WaveConverter32" in "Forum->Nintendo 3DS Roms, Homebrews and Downloads->Other Nintendo 3DS Downloads->Nintendo 3DS PC Applications" Forum.
Then drag all those things (besides the Convert.bat, that's his own custom tool to convert, if you'd like to do that) where ever you need the converter.