Time machine only backs up one internal drive

I have a Mac Pro Early 2008 running 10.8.5 with 3 internal drives. Time machine sucessfully backs up the 600GB boot drive but has stopped working with the all important 3TB Data drive (half full). The remaining 4TB drive is for Time machine backups. Only the boot drive now sucessfully gets backed up with Time machine backups but not the Data drive.
I have tried everything I can to try to get it to work again and here are some of my steps taken:
- Checked to see if the Data drive has not bee excluded from Time machine backup options. No it hasn't been excluded.
- Check Smart Status on all drives - all good.
- Use Disk Util to verify all my drives - all good, no errors.
- Stop Time machine, formatted the Time machine backup drive and restarted Time machine. Still not backing up my data drive.
- Reset Time machine by following http://pondini.org/TM/A4.html - Still no change.
- Remove the Data drive from Spotlight indexing with Spotlight - privacy settings and then re-add it to Spotlight indexing - Now it does a full backup, but no more incremental backups are created when files on the Data drive are changed. And the full backup of the Data drive disappears from the Time Machine backup a few days later!
The Time machine logs just shows - "Will copy (Zero KB) from Data".
I have tried to follow the troubleshooting hints on http://pondini.org/TM/Troubleshooting.html but can't seem to find any other clues to help me with my problem.
Does anyone else see this before and have any suggestions?

I've tested these instructions only with the Safari web browser. If you use another browser, they may not work as described.
Triple-click anywhere in the line below on this page to select it:
{ diskutil list; echo; diskutil cs list; } | open -ef
Copy the selected text to the Clipboard (command-C).
Launch the Terminal application in any of the following ways:
☞ Enter the first few letters of its name into a Spotlight search. Select it in the results (it should be at the top.)
☞ In the Finder, select Go ▹ Utilities from the menu bar, or press the key combination shift-command-U. The application is in the folder that opens.
☞ Open LaunchPad. Click Utilities, then Terminal in the icon grid.
Paste into the Terminal window (command-V).
A TextEdit window will open with the output of the command. If the command produced no output, the window will be empty. Post the contents of the TextEdit window (not the Terminal window), if any — the text, please, not a screenshot. The title of the window doesn't matter, and you don't need to post that.

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