I am not sure exactly what the scenario you have is, but if RadToolTIp is instructed to get content from a custom location (i.e. AjaxUpdate event handler) it will not modify the target element, so its title/alt attribute will remain in place and the browser will show it. In this case you may want to avoid rendering this attribute (it corresponds to the ToolTip server property WebControls have).
If this is not what is happening in your case I would advise sharing a small sample of your logic so we can inspect it and see what is going on.
If you want to get updates on new releases, tips and tricks and sneak peeks at our product labs directly from the developers working on the RadControls for ASP.NET AJAX, subscribe to the blog feed