When a pane goes floating, the pane is removed from the group and it's placed inside a new group inside ToolWindow. Maybe this causes the problem.
We have an example how to implement RadDocking with PRISM here - http://blogs.telerik.com/xamlteam/posts/13-12-11/using-raddocking-with-prism-in-wpf-silverlight
. Please, refer to it and let me know if this helps.