After disk failure I had to re-install whole system (Debian 6.0.6) on a new one. I installed all packages from this tutorial: http://www.howtoforge.com/perfect-server-debian-squeeze-with-bind-and-dovecot-ispconfig-3 and installed ISPConfig (ISPConfig version: 3.0.4.6) I just replaced whole /etc and /usr/local/ispconfig with backed up config from old disk. Everything seems to work, but the logs in ISPConfig Monitor stopped refreshing and all show 'Data from: 2013-01-14 13:00'.
Please see debug instructions here: http://www.howtoforge.com/forums/showthread.php?t=58408 the server.sh script is also responsible for refreshing the logs. You will have to run te test at a time where the "Current Minute" can be devieded 5. E.g. 05, 10, 15, 20 etc.
Do I need to run it at the first second of the minute? I ran it at 10:30:29 and it returned just 'finished.'.