Without seeing your code, I can only guess of course...
It sounds like you're saving the state of the new dock before it gets its state from having been docked. As such, I would suspect that you're doing this too early in the page lifecycle. It's like loading a datagrid during page load, deleting a record during a postback event, and then seeing the deleted record still in the datagrid.
You might want to trigger the saving of your dock states in the SaveDockLayout event. I was hoping to find some information online about the dock lifecycle, and I did. Check out RadDock in the Page Life Cycle
. I found that very helpful, as well as the article, Dynamically Created Docks
I hope that helps.