I'm using MediaWiki 1.22alpha (741637f) and when I use ResourceLoader to load CSS files, IE9 ignores all the Media Queries and activates all the styles even when they don't apply. This is true both if the queries are specified inside the one of the CSS files e.g. '@media all and (max-width:1000px)', as well as when specifying the media query in the skin via: 'styles' => ['a.css', 'p.css' => ['media' => 'print']]. I don't seem to have this problem with IE8 or IE10. When I set ?debug=true so that the CSS files are loaded separately and normally, the problem disappears.
Topic on Talk:ResourceLoader
Appearance