Oh, you're doing it wrong; you need to type in the name of your book after. So something like
Code:
kepubify.exe --inplace --calibre book.epub
if kepubify and your book are in the same folder. If the book is in a different folder, you'll have to type out the entire location of the book (ex. C:\path\to\book.epub).
geek1011 also answered your question in the
version 3.0 thread. Just copy/paste what he wrote into a file named kepubify.bat and drag your book onto that instead if you don't want to type things out manually.