I'm reposting this as a bug since currently when multiple windows are created, the zIndex never gets adjusted like in telerik.window.js hence it is impossible to have dynamically created windows without having to fix the zIndex manually for each new window. And once you adjust the zIndex on one window, it always stays on top.

Original post with comments:

http://kendo.uservoice.com/forums/127393-kendo-ui-beta-feedback/category/31821-bugs