Setting position:relative to a container so high in the page structure will mean that all elements on the page that use some sort of positioning (like the notification) will be relative to this element. The other CSS properties you add to it only make the behavior easier to spot, as otherwise this div would match the form element.
RadNotifiacation renders its popup as a direct child of the form element and is, therefore, relative to the form when positioning itself. This is how the control works and this allows it to position properly in most scenarios, so it relies on this. What you have done is to change the positioning of the entire page and thus changed what the notification relies on.
What I can advise is that you either move this relatively positioned container inside the form so you can still keep your other layout in place, or remove the animations so that the position of the notification does not change. Animations simply change the control's lifecycle and positioning for a while (until they complete) and this cannot be avoided in another manner than disabling them.
All the best,
the Telerik team
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