Just as an update, I tried deleting the com.apple.TimeMachine.plist preferences file and effectively 'resetting' Time Machine but it made no difference. I ran the diagnostic and reported it as a Bug to Apple. For your info, details of report are below.
Thanks
Andy
20-Aug-2013 10:42 AM Andy Worby:
Summary:
Time Machine is failing to back up all top-level folders present on the main OS hard disc, even though they do not appear in the 'Exclusions' list within Time Machine preferences. As a result, 'System', 'Library' and 'Applications' top-level folders are not backed up. The only folder being backed up is 'Users'.
Upon investigation, the com.apple.TimeMachine.plist preferences file contains exclusions for above mentioned top-level folders (see screenshot 1), although they have 'not' been purposefully added to the 'Exclusions' list via the Time Machine preferences window.
Deleting the com.apple.TimeMachine.plist preferences file and then setting up Time Machine once again via the preferences window does not change the result - the three affected folders still fail to back up.
Steps to Reproduce:
1. Delete com.apple.TimeMachine.plist preferences file to perform a full reset of Time Machine.
2. Enter Time Machine preferences window.
3. Select backup hard disc ( in this case, I am using an external 2TB hard disc via Firewire 800 connection).
4. Click options
5. Ensure that only the backup hard disc is selected in 'Exclusions' list.
6. Click Save
7. Commence a Time Machine backup.
8. Allow backup process to complete.
9. Go directly into the backup hard disc.
10. View top-level folders that have been backed up from the OS hard disc.
Expected Results:
All top-level folders from the OS hard disc should have been backed up.
Actual Results:
Only the 'Users' top-level folder from the OS hard disc has been backed up.
Regression:
Problem is continuous, and has occurred for some time, although I do not know from which exact date.
Notes:
I have included the following attachments:
1. Study iMac.tmdiagnostic.zip
2.Screen shot 1 - this is a screenshot of the Time Machine preferences file
3. Screen shot 2 - this is a screenshot of the top level folders within my OS hard disc