This happens only when using XBAP Full Trust Application. Initially when floating a pane with mouse, the ToolWindow is misplaced. If the user release the dragged window and click the header again, works fine.
Changed the status to Won't fix as XBAP (XAML Browser Application) is no longer supported. For more references read http://docs.telerik.com/devtools/wpf/installation-and-deployment/installation-system-requirements-wpf.html