I think it might be the iTunes 11 update, and not any update on the shuflfe, that is causing your problems.
You probably need to show the sidebar, which the new version of iTunes can hide (to make the app more streamlined). From the iTunes menu bar, under the View menu, select Show Sidebar. With the sidebar visible, iTunes mostly works like it did before the latest major update.
If that's not it, please post back.