On the following website, when I click the dropdown for the Login at the upper right, it is displayed behind the silverlight map. I can't use windowless mode because this would disable scrolling and menus on the map. I have tried putting the z-index everywhere, but I can't seem get it to work.
This will not be possible without using windowless mode. The Silverlight plugin is going to get rendered on top. You will just have to put the map lower to give the login more space or else deal with the limitations of windowless mode.