Hello Tom,
I assume that you are using a RadWindow with ContentTemplate and you have wrapped it in the ajax panel as follows:
If so, the ajaxification will not work correctly because in this configuration the content of the radWindow is moved in the DOM and MS AJAX has limitation with this because it uses innerHTML (our RadAjax is also based on MS AJAX).
What I suggest is to move the ajax panel inside the RadWindow - in this manner you will ajaxify the content of the RadWindow and not the whole RadWindow (which is the thing actually needed in most scenarios):
I hope that my reply is helpful, let me know how it goes.
Best wishes,
Svetlina
the Telerik team