Yeah, the menu being invisible unless hovered over was an intentional choice. I've always been an avid advocate for the death of all menubars. I could see how people would be hassled by this, but really, I've mostly created this skin to suit my own personal aesthetic preferences.
I like the auto-hide idea you have stephen, I think it would really make the whole interface look a lot nicer, and would definitely give musicbee another advantage to other music players like songbird or itunes.