Hey kellogg9, I’ve noticed this bug also, and it’s a bit of a pain. After digging around a bit I found this:
Around line 71 of wp-minify.php (v1.1.8), change:
add_action('wp_footer', array($this, 'post_content'));
to:
add_action('wp_footer', array($this, 'post_content'), 20);
This makes the post_content function fire later in the wp_footer order, after WordPress has added the footer scripts rather than before. Be aware though, this works great for me on a local MAMP server, but I’m still debugging an error on a remote server. But that may be due to the remote server being really badly set up. My error log shows:
PHP Warning: filemtime() [<a href='function.filemtime'>function.filemtime</a>]: stat failed for /home/blahblah/public_html/site/wp-content/plugins/wp-minify/cache/b05f93d5c0524ecf706ed37d91e76733.js in /home/blahblah/public_html/site/wp-content/plugins/wp-minify/wp-minify.php on line 625