Comment 1 for bug 45589

This similarly happens to me, with the primary difference being that in Layout Options I set "Press any of Win-keys to choose 3rd level" (making mine <mod5>). That is the only Layout Option selected that is not default. The problem seems to only happen after I assign <mod5>t to Terminal, but even removing it does not allow other shortcuts to use <mod5>.

All the other shortcuts I've tried will not work with <mod5>, those being Search, Launch web browser, email, Home Folder, and Launch Calculator, and I suspect none of the others will work either. Changing these back to a non-<mod5> shortcut lets them work again, but even changing them back to <mod5> does not make it work.

If any more information is needed, I'll be pleased to help as much as I can.