I noticed that adding in styles w/ jQuery in IE9 works fine however this just doesn’t seem to work:
box.css({'-ms-transform': 'scale(.2)'});
although when I try to do that w/ any other vendor prefix -webkit-/-moz-/etc it works fine… does it need to be applied differently for IE? (the scale is dynamic hence the reason i’m doing it in js and not in css)
just checked it on the last few versions of jQuery and it seems to be working fine there must be some other issue with your code. did you check to make sure box.length > 0 ?
here’s the test page: http://jsbin.com/ehasuz/edit#javascript,live
hope this helps -ck
edit: just cause i feel like we are not all on the same page with the demo

this would make me hazard a guess that your problem is somewhere else, unless there is a case where ie9 optionally applies css3 transforms..
hope this helps -ck