hamiljf,
Yes, that is weird. I can replicate some of the issues but it’s very inconsistent. The problems are more noticeable with a new workspace (I tried with the menu on the title bar and no menus would drop down). I see similar things in the base eclipse, so will raise a bug with eclipse, though, as you mention, it may be a Unity problem.
What makes it look more like a Unity problem is that the workaround mentioned in this FAQ (workaround 2) does work. It causes the menu to be displayed within the application window (in the old way) and it acts fine, with no unexpectedly disabled menu items, that I could see. So that would be a fix for you, for now.
Please let us know if that workaround works for you.