I have this same issue. I am working off WordPress 3.8 and I have the latest WP E-Commerce and Gold Cart plugin. I am using the “Awake” theme by MySiteMyWay and disabling the theme and using the default wordpress theme makes it so the fancy notifications appear, but switching back to my original theme makes them hidden again.
I never had this problem on previous versions, and I do not have the luxury of easily switching themes. Is there any thoughts about what specifically could be hiding the plugin? I can’t quite see what the error is.
Thanks!