If you place on a web page a ModalPopup and a Silverlight control, you might end up with the ModalPopup hided by the Silverlight control.

To avoid this at the time you call Sys.Silverlight.createObjectEx you need to give the following property to true:

isWindowless:’true’, // Determines whether to display control in Windowless mode.

And then everything works again and you see your ModalPopup.