I assume this doesn't happen on the default style? I recommend some systematic troubleshooting. If it doesn't happen on the default style then start reverting custom templates and CSS in your custom style until you isolate the problem. If you continue to have problems then I can take a look if you give me admin access.
A couple, but none of the templates in the Default style have been customized.
I'm at a loss here, I can clearly see by using Chrome and inspecting the element that something is wrong.
If I disable the z-index: 7500 in the .Menu CSS class, it uses z-index from the .PrefixMenu instead (which has a z-index of 15000),
this makes the prefixes show up in front, but I have no idea how to solve this, I've been looking through the templates and I see nothing that stands out.