The AjaxControlToolkit ModalPopupExtender has a very high z-index value - 100 001, so in order to show a tooltip above it you would need to make its z-index even higher (it defaults to 8000). Details on the default values and a way to change it are availalble here: http://www.telerik.com/help/aspnet-ajax/controlling-absolute-positioning-with-zindex.html
. Here is a CSS alternative that will change the RadToolTip's z-index. You can find a similar rule that will reduce the modal popup extender z-index if you want
If neither helps I would advise sending us some code that can show the problem so we can actually investigate it.
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