I had this same problem but somehow it went away when I went with a longer stem (100 to 110) and changed wheel sets from Ultegra/Open Pro to Kysz Elites. I cannot explian why but this fixed my problem. I know the Elites sure are more laterally stiff and they made my whole bike feel better. I think the longer stem put more weight over the fork so this may have also affected the shimmy problem.
tommy