Hi. I actually fixed this myself by converting all the tweens to relative tweens like this:
var i = 0;
var a = 1;
var d = .5;
var d2 = .55;
var d3 = .56;
var t = .5;
var tt = .25;
var e = Power2.easeOut;
TweenMax.set("#container", {alpha:a, ease:e});
TweenMax.to("#jacket", t, {top:"+=35", left:"-=20", delay:d, ease:e});
TweenMax.to("#helmet", t, {top:"+=66", left:"-=14", delay:d3, ease:e});
TweenMax.to("#goggles", t, {left:"-=105", top:"+=10", delay:d2, ease:e});
TweenMax.to("#boots", t, {top:"-=6", left:"+=16", delay:d2, ease:e});
TweenMax.to("#shirt", t, {top:"-=5", left:"+=98", delay:d, ease:e});
TweenMax.to("#shoes", t, {left:"-=40", top:"+=2", delay:d2, ease:e});
//TweenMax.to("#hat", t, {x:-100, delay:d3, ease:e});
TweenMax.to("#txt1", tt, {alpha:i, delay:2});
TweenMax.to("#txt2", tt, {alpha:i, delay:2.1});
TweenMax.to("#txt3", tt, {alpha:i, delay:2.2});
TweenMax.from("#txt2_1", tt, {top:"+=25", alpha:i, delay:2.3});
TweenMax.from("#txt2_2", tt, {top:"+=35", alpha:i, delay:2.4});
TweenMax.from("#bar", tt, {top:"+=35", alpha:i, delay:2.5});
TweenMax.from("#txt2_3", tt, {top:"+=35", alpha:i, delay:2.6});
TweenMax.from("#cta", tt, {top:"+=35", alpha:i, delay:2.7});
Hadn't had this bug come up before which is why I was interested - I do have a question about backgroundPosition in IE9 but I'll make a seperate thread sometime.
sorciereus's post in IE9 position tween issues was marked as the answer