I have minify turned on and it appears to be working for HTML minificaition, but with CSS and JS it does not appear to actually do anything. I have a bunch of CSS and JS files selected for my current theme and I've tried checking and unchecking different options for both, does not appear to make it work.
Additionally I get this message. Not sure if it's related, but I didn't get it when I first installed the plugin a few weeks ago:
"Recently an error occurred while creating the CSS / JS minify cache: Some files were unavailable, please check your settings to ensure your site is working as intended."