After further investigation it seems that the previously known issues is a limitation of the current implementation of the RadWindow control and unfortunately we are not aware of any workaround for it.
The issue is caused by the way the ToolWindows (RadWindows) are brought to the front in the Silverlight framework. In that framework when a ToolWindow needs to be brought to the front when focused that ToolWindow is closed and reopened immediately. Because of this functionality the first mouse click is captured but lost when the Window is closed and the Click event is not triggered.
Again we apologize for any inconvenience that this maybe causing.
the Telerik team