I had the same error when i try to upgrade from 1.9.8 to 2.0 Prev3. See my post http://moodle.org/mod/forum/discuss.php?d=149899.
The problems were missing files in the data directory. As you has mentioned, your test system comes without any user data. So i think there is your problem. Moodle 2.0 has a complete different structure for user data files. During the update process all resources are check for inconsistencies.
Best regards,
Mathias
Testing and QA
Moodle 2.0 preview 4
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