You can create a keyboard shortcut by simply opening the properties of the X1 shortcut in the start menu - there should be a "Shortcut" tab, where you can enter any shortcut you like, you are not limited to Ctrl+Alt,
and that shortcut will work at any time.
As for the shortcut set from X1 that does not work - there can be two reasons - either the key was not being correctly re-registered on Windows startup, or it failed to launch the UI. Can you please check the X1ServiceHost.log for any messages or errors with "X1UILauncher" in them?
Jogy