Why can I not make a back up copy of Zero Hour?
Each time I copy the game using the protected game format I get the message, please eject and re-install correct cd?
I thought Clone could copy anything?

who knows, who knows...?!?
you try to play the copy out of your burner?
it definitely cannot, but no software can copy ANYthing...

I have tried to play the copy on another pc and in another drive but the same message

but, are you trying to play from burner-devices or from true -ROM drives?
if you want to play from burner-devices, you have to enable the ATIP-hider - CCD has this feature in the tray icon, but i don't know how it is called exactly, as i don't use CCD. something like 'hide CD-R media' or similar should do it...
btw: you should read / write the disc @ 4x speed, as this gives more accureate results...