Those results are a bit weird cos from that test it looks like the multidimensional array is faster. I think this is because it takes time for Flash to evaluate map2[0*w+j] for the flat array.
Also, I downloaded your Flash 9 source (which is AS2 by the way) and modified it for AS3 and it still looks like the multidimensional array was faster.
Even more argument to use multidimensional then...