I have been working with SharePoint quite a bit over the past few months. At Netstore we are building an AA accessible website for our client using XHTML with a CSS based layout.
function MSOLayout_GetRealOffset(StartingObject, OffsetType, EndParent)
if (!EndParent) EndParent=document.body;
for (var currentObject=StartingObject; currentObject && currentObject !=EndParent && currentObject != document.body; currentObject=currentObject.offsetParent)
var offset = eval('currentObject.offset'+OffsetType);
if (offset) realValue+=offset;
So if you ever experience the problem, copy and paste this function into your master page file, anywhere after the SPWebPartManager and it should stop.