I am making this a community wiki, for three reasons:
I had a similar problem with an accordion in IE6 and IE7 where I was not using the default HTML structure for the accordion. Strangely enough, fixing the horizontal size of the accordion elements to a certain number of pixels cleared up the problems with the accordion animation. Why? I don't know. But I observed that the problems were specific to using autoHeight: true and the problems occurred at the end of the animation where I assume the height of the accordion elements is reset. And we all know IE cannot do math.