I have a similar problem: after upgrading 16.04 to 18.04, custom keyboard shortcuts no longer work, also language layout switch shortcut doesn’t work. I have several keyboard shortcuts to launch certain programs, they are set up in Keyboard > Shortcuts > Custom Shortcuts and completely ignored currently. For language layout switching, I tried “tweaks” app, also the solution with custom ppa above, nothing seems to help 
it’s really disheartening.
I’m using Unity, not the default GNOME - the header takes up room for no reason in gnome and there’s no way to get rid of it, so I’m sticking with Unity… I really hope the keyboard shortcuts can be fixed.
One weird thing I noticed is that when I click on current language indicator in the top bar and then Keyboard Layout Chart, the keyboard layout window changes Shift background to orange when I press it, and Alt background to orange when I press Alt, but when I press Alt and then Shift (the way I switch between languages), the orange background disappears on Alt after pressing Shift. For Ctrl+Shift it works as expected - i.e. both are highlighted, but Alt+Shift shows no highlight… I will really appreciate help fixing the shortcuts, I can’t really work without them and I’m considering downgrading back to 16.04 (I keep asking myself why I upgraded, everything worked perfectly!)