If a popup contains a Datefield the corresponding datepicker is opend behind the popup-window. On other browsers than IE the Datepicker is rendered in the front but the modal-window-layer is rendered behind the first popup, so the first popup is not disabled.
This is a little tricky as there seems to be a dependency to the way, the popup is used. This can be reproduced in your demo: http://tobago.atanion.net/tobago-example-demo/faces/reference/popup.jsp
The popup opend via the menu shows the problem at once (popup is opend via popup-reference). If you open the popup via the Open button (popup is a facet of the button) the calendar first works fine. But if you than press ok (without filling the required field) the calendar is opened behind the popup.
A similar problem exists with the InputSuggest-Layer for an InputField in the popup.