I just wanted to share this, in case others meet the same issue.
Our elements have values set for various prefixed and non-prefixed CSS properties (set on the element.style.) For example:
element.style['-webkit-transform'] = "scale(2.0)";
element.style['-moz-transform'] = "scale(2.0)";
element.style['transform'] = "scale(2.0)";
When the polyfill starts to interpolate a value, it will only set the transform property because that was the property it detected was available when it ran detectFeatures(). However, when both properties are present, it appears Chrome (36) will actually take the value of -webkit-transform to transform the element, and not the value of transform. As a result, the animation does not appear in Chrome, because Chrome is reading the un-animated property!