[Answer]-Django-pipeline producing empty files

This led me to the answer:
http://www.daveoncode.com/2013/09/19/configuring-django-pipeline-by-using-closure-compiler-for-javascript-files-and-yui-compressor-for-css/

Looks like the binary needs to be the exact command used to run the binary. In this case it should have been:

PIPELINE_YUI_BINARY = "java -jar C:\\path\\to\\the\\yuicompressor.jar"