I had an issue with Munin stopping updates after I did any configuring of websites. It was tracked down to the security setting for the server set at high in ISPConfig 3. This was changing the permissions of the web folder to 710. As the munin folder is under the web one and is written to by user munin it was getting denied by this setting. Changing the security setting to medium fixed the issue. Another possibility is to install the munin directory somewhere else.