discuss.answer
I sussed out what I was doing wrong.
To concatanate and minify more than one css file the files need to be in the same directory and be called like this:
<link rel="stylesheet" href="[[SmartOptimizer?&files=`assets/path/file1.css,file2.css` ]]"/>
I was calling it like this:
<link rel="stylesheet" href="[[SmartOptimizer?&files=`assets/path/file1.css,assets/path/file2.css` ]]"/>