[oXygen-user] XSLT issue

I have a stlyesheet I use to clean up SVG files. I have a transofrmation scenario created that uses Saxon 9EE (I have a license for Saxon as well). The transform runs in oXygen and produces the expected output. However, when I run Saxon from the command line, all I get in the output is the XML header. What would cause the command line execution to produce different results to the in-application transformation?