Need more info. Do u have a link to your site to see what is going on? Is it in fact minifying your root domain page when u look at the page source and pagespeed is still complaining?
After looking at this plugins code i know it doesnt minify as efficiently as one would like which is why a few of us made our own forked version that shrinks the final size even more.
The biggest mistake the author made is purposely putting in linebreaks due to his own preference (he hates looking at minified pages that dont have CRLF). That to me is quite possibly the dumbest thing i've ever seen. For a plugin that brags about shrinking pages why would the author get all emotional and subjectively add CRLF because he doesnt like the visual appearance of the result? Wouldnt that contradict the very purpose of the plugin? We were baffled by this and a few other silliness so we corrected them. But overall, putting these author intentional flaws, the plugin is better than the others i've tried..which is why i still use it...my own forked version of it that is.