I have a similar problem.
Currently using Ebox 1.4, and wanted to upgrade to Zentyal 2.0-3.
As there is no upgrade path, I installed zentyal on a new server hoping to import the old config once all the relavant software modules are added.
However when I try to import the config I get this error:
Some error has happened in Zentyal:
Cannot restore because user root already exists as system user. Delete or rename this user and try again
Why is zentyal even trying to import the root user? Root user cannot be renamed, so therefore its impossible to import the config.