Thaya,
I noticed the changelog where you told that the "having wordpress installed in a subdir" was fixed but I just downloaded the latest version and still got the problem.
The issue is in get_css_location and get_js_location.
I saw you get the prefix defined in WP-Minify settings page and removes from the $src string. You dont need to put a Setting just for prefix since this can be retreived by wp functions.
I changed
$site_url = trailingslashit(get_option('siteurl'));
$num_matches = preg_match('/^https?:\/\/.*?\//', $site_url, $matches);
$domain = $num_matches>0? $matches[0] : $site_url;
To
$domain = get_option('home');
And its working. I admit I hadnt the opportunity to test with files generated from inline stuff, but I'll soon.
Im working also on activating the PHP Minfiy's feature of adding an far future expires header, but it still a little buggy.
Tried to find an address to email you, but couldnt find it.
I see you've been busy these days, maybe I can help you with some issues.
Regards!