I can't seem to replicate this with your demo site - but am hoping someone can point me in the right direction.
We are using the Metro theme - with the default AjaxLoadingPanel control.
In Chrome (latest standard release), when zoomed at 100% the AjaxLoadingPanel always appears exactly over the control it is supposed to. If you zoom in - it still works - so long as you have not scrolled down the screen at all. As soon as you scroll down the screen - even slightly, then execute a callback that will display the AjaxLoadingPanel, and its position is offset downward by the scroll distance of the page.
This same issue happens with RadWindows that are set to open and autosize to the center of the browser. In the same scenario - they get pushed to the bottom of the screen - and if you try and drag them up - they snap back to the bottom.
We are trying to track down what could cause this - but not sure how the toolset is deciding where to place things?