In order to make automatic scrolling, the fixed columns/rows (top, left, right, bottom) of FixedHeader need to be accounted for in the calculation of the new scroll position.
Since each of the fixed elements is wrapped inside a div it's is easy to determine its dimension. In addition to the dimension the position of the table needs to be accounted for. fnGetSettings().oMes of fixed header could be the right source, I think.