The behavior is happening with protostar and the menu item is pointing to that template. That was the first thing I've checked.
I'm stumped on this too because in anytime I've used cb on the same hosting this hasn't happened. Without CB core installed, the css for menu items works perfectly regardless of the template. That's the only differing element I can see.
I should of been more specific, it was a CB Registration Form Menu item not the standard joomla one.
I'll try tech support with the hosting and ensure it's not some strange caching thing on their end that is somehow conflicting.