Comment 4 for bug 1194708

When this happens *may* be worth seeing what .desktop is associated with the ? icon. That can be done by temp locking it to the launcher & looking at com.canonical.Unity.Launcher favorites in dconf-editor
On some occasions it's been nautilus-autostart.desktop, others just nautilus.desktop

The later can be caused by an improper nautilus .desktop in ~/.local/share/applications, the former no clue why