To be complete and follow your instructions precisely, I took another look at the ISPConfig not writing changes to disk section.. I was happy that my memory of the article was correct, it gives instructions only for those affected servers who are running the web gui. Page two of the howto which covers installing on the secondary DNS has the users set it up without the gui. I also agree with this logic, there is no need to have web interfaces everywhere.
The debugging guide covers all kind of setups, it does not matter if you have a single server or a few hundred servers as the instructions are the same. So please follow the debug instructions if you like to get help with your issue.
1) Enable debugging in the ispconfig interface (which is on the server that runs the interface of course)
2) Run the server.sh script on the server that is not writing the changes.