I have exactly the same problem.
I have tried deleting prefs as well - no go.
However if I quit cubase, then open it again and start a totally new blank project, it works.
But if I then close the test project and open the ongoing project, no go.
It;s a real drag not to have a click track pumping away when recording to a tempo based project that speeds up /slows down etc.
Any help please?