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Old 2nd April 2013, 12:24
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So, it would appear that the problem might be the fact that I did not install ISPConfig on an empty server?
Yes, that might be the case as your manual configuration conflicts now with ispconfig.

It is possible to fix that most likely without a reinstall but it requires some debugging of the apache configuration. Please post the output of:

netstat -tap

and

iptables -L
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