1) Did you delete all secondary zones in ispconfig like I suggested?
If no, then do it now.
if Yes, then you have a general problem with your ispconfig multiserver setup, e.g. the /etc/hosts file was not configured in the way described in the tutorial before ispconfig was installed on the master and slave server. If the file is not setup corrcetly before you install ispconfig, the sync must fail later as the slave server is not able to conect to the mysql master database then to get the required domain infos for the sync.
To test this, enable loglevel debug for the slave server in ispconfig, disable the server.sh script in the root crontb of the slave and run it manually. See sticky post in this forum for detailed instructions.