Update on my problem, found a solution that may work for you: I had the same problem in that backup fails at random databases with a "Unknown error". Through experimenting, I realised that Application Loader creates a backup (provided you check off the box under options in the App Loader screen), even if you're failing to complete one. To verify this, you could install a random app through App Loader, and try locate the backup created on your HDD.
After that, I went on to do a full reinstall of the handheld OS using App Loader, checking off the backup handheld, delete all applications and data boxes. Immediately after the device data was restored, I could do a full backup with no issues. I then tried again after Enterprise Activation and it's still working. If this approach might help, do try it out.
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