By saying that the server side methods of the RadTreeList should properly fire no matter if ajax is enabled I mean that the ajaxification of the control would not prevent the server side methods to work correctly. Therefore I'm not completely sure what exactly is causing the issue on your end. It will be best if you could open a regular support ticket adn send us sample runnable version of your application which demonstrates the problematic beahvior, Thus we will be bale to test it locally and advise you further.
Meanwhile you could review the online demo below which demonstrates the correct behaviour of DragDrop functionality in ajaxified TreeList control:
the Telerik team
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