The problem with the dropdown occurs because the element will be initialized twice when used in the window. At least for now in order to avoid this problem, you should either load the window content with Ajax using the LoadContentFrom method or initialize the dropdown with the jQuery plugin.
Regarding the TreeView, it offers built-in support for checkboxes by using the CheckBoxes method. Please check the checkboxes demo in the offline examples project which is included with the installation.
the Telerik team
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