Upgrading to from 16.04 to 18.04 ran smoothly, but some customised keyboard shortcuts have stopped working and the problem seems to be with the commands attached to the shortcuts. Strangely, for instance a shortcut to run thunderbird with the command "thunderbird" worked immediately after the upgrade, but I changed the keystroke and it no longer works.
Running the command from the command window (opened with Alt or Alt+F2) also fails. Several other shortcuts/commands display the same behaviour.
The solution appears to be enabling commands. In compizconfig-settings-manager, tick the first box, 'Commands'. Has the default changed? Somewhat mysterious how the commands 'left behind' from 16.04 worked, but new or modified commands failed.