I got a reply back from Xara Support and, yes, there is a bug. But it appears to be related to publishing from XaraDesigner6 when ALL LAYERS VISIBLE is enabled in the Page and Layer Gallery.

"The problem we I'm seeing with your file is somewhat different to what you described ....

With all layers visible ENABLED in the layer gallery, the popup behaviour is NOT working as intended.

With this option DISABLED ( all layers visible not enabled from the page and layer gallery) the site exports and behaves as intended." Customer Support.