Embedded XML->PDF performance vs CLI: Why so slow?

This is also posted on SO[1], with the code. 

Using XML and XSL, in less than a second the CLI program produces 
the desired PDF. My embedded program in Clojure, which follows the 
example code (ExampleXML2PDF.java)  closely, uses the same XML and 
XSL to produce the same PDF -- but it takes it around a full 
minute. I've tried sifting through the example code to find places 
optimizations occur, but I'm hoping someone here can help me know 
how to get around the tremendous time sink that seems to occur 
with my transformer.transform call. 

Thanks,
- Tory

Footnotes: [1] 
http://stackoverflow.com/questions/36802128/embedding-fop-xml-to-pdf-why-so-slow-vs-cli