I have a similar issue where all post URL's are gzip'ed, but javascript files like /wp-includes/js/jquery/jquery.js?ver=1.10.2 are not compressed. Same goes for CSS.
In General Settings 'Minify' is enabled in manual mode. In the Minify settings tab, the both JS and CSS minify settings are checked (so must be activated), also Minifying the JS in the <head> section.
In the Browser Cache settings tab HTTP (gzip) compression is checked in the General, CSS&JS, HTML&XML and Media&Other Files boxes. So all together my gut feeling says settings are correct. However the results are the only HTML is compressed (according to both http://www.gidnetwork.com/tools/gzip-test.php and webpagetest.org).
What to do?
