The problem appears to be fixed but has brought in other issues.
I ran Onyx on the Macintosh HD not the clone (or was I supposed to run it on the clone?)
After running Onyx and the rebooting from the clone all was well until I went to the prefs to select the Macintosh HD to boot from and it was not there
!! I then chose to restart holding down the option key and then saw both drives with the Macintosh HD highlighted on the left and the clone not highlighted on the right with the pointer frozen on the screen. I hit the return key and it started up from the Macintosh HD. Obviously concerned not seeing the Macintosh HD, I repaired disc permissions on the Macintosh HD and it shows this
:
Permissions differ on “usr/share/derby”, should be drwxr-xr-x, they are lrwxr-xr-x
Repaired “usr/share/derby”
Warning: SUID file “System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAgent”…has been modified and will not be repaired
What does the permissions log mean and how to deal with it?
What else should I do "to live happily ever after"
Many thanks for your help