I think the problem you're hitting is precisely due to the use of the RadAjaxPanels (or ASP.NET AJAX UpdatePanels, more generally). In particular, when you use an UpdatePanel to ajaxify a postback event on the page, only controls contained within the panel can be updated after the ajax event complete. To update controls on other portions of the page, you have to start configuring triggers.
Now triggers can be a messy game, especially when you're dynamically adding UserControls to the page. With the RadAjaxManager, though, there is a more elegant solution.
On your application's MasterPage, you can add a single RadAjaxManager control. Then on all of your content pages and UserControls, you can add RadAjaxManagerProxy controls to configure the ajax settings for each page element. At runtime, these settings will be rolled-up to the primary AjaxManager and automatically define all necessary UpdatePanels and Triggers on your page to correctly update page elements.
I know it could require some conversion work now, but in the long run this will make your application much more maintainable. The basic problem with the current architecture is that UpdatePanels (and in turn RadAjaxPanel) are not designed to allow you to update controls outside of the panel on an ajax request. If you absolutely
don't want to improve your architecture at this point, there is a way to script the interaction between multiple RadAjaxPanels. See this page in the docs for specific guidance:
Hope this helps!