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Old 19th January 2010, 12:39
till till is offline
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The problem was that you run the setup script a second time without creating the /root/ispconfig folder before. So the setup assumed that no ispconfig is installed and it was run in install instead of update mode.

Take a look in the /tmp and /root/ folder if there are any backups as ISPConfig makes a backup before it upgrades the server.
Till Brehm
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