Interface tries to intelligently rearrange itself, and ends up annoying user? Reminds me of that old MS Office "feature" of hiding unused menu items, which bugged me like crazy.
Yeah, it really makes me feel paranoid that the item I want will be hidden when the menu is shown, so I always expanded it (until I turned it off entirely).
I'm probably the only one who feels the same way about hidden tooltray icons, too, but I usually expose them all on Windows.