I think the following two issues are related:
1) ALT-rightclick, Super-rightclick etc. have no effect on the gnome panel.
2) I cannot set certain shortcuts using System Settings -> Keyboard -> Shortcuts. For example, the ALT key is recognized as "Level3 Shift", and cannot be combined with any other key for a shortcut. The Windows key is recognized as "Multi key" and again cannot be combined with other keys.
I'm using Gnome Classic on Ubuntu 16.04. Gnome Version 3.18