In the particular scenario, it is exactly this that is happening. The correct way to go would be to place UpdatePanels inside the RadDock controls. The result would be that RadDock will work fine, and AJAX will work fine. However, if the RadDock objects themselves are expected to be both moveable around the page AND be updatable from their original UpdatePanel - this will not work out of the box (at least for now).
We are currently investigating a possible workaround that will "trick" the MS Ajax framework into "believing" that docks are where they were when the page was loaded. However, even if this succeeds, it will be a hack of the framework, rather than a correct, reliable solution.
As already stated, we have concentrated our main developer efforts on the Prometheus control for feature enhancements and improvements whereas "regular" RadDock will receive only basic fixes. That is why, the "trick" we are working on will only be implemented in the Prometheus RadDock. I cannot tell you when this will be ready, but as many people ask for it, we will do our best to implement it for SP2, scheduled for the end of February.
the Telerik team