The Load/Save layout of the docking component does not support serialization of inner controls. In your scenario maybe this causes repositioned panels to be initialized as new objects. This is why their Controls collection is empty.
The solution is to use the approach described here: http://www.telerik.com/support/kb/article/b454K-mcd-b454T-ckg-b454c-ckg.aspx
If you have additional questions, please contact us.
the Telerik team