Ohhh I get it now. I downloaded the release version of ISPConfig 3.0.1 but I did the svn export to the install directory as in the Perfect Server guide. I guess I did not read clearly enough. I just did the steps and didn't realize there was an option at that point.
I manually imported the sql file to phpmyadmin. The lines I removed from the file seem to only try to import the database. I don't believe they do any sort of updates to it but if they do then I guess my install is messed up anyway.
So far ISPConfig seems to be working. There are some issues with it but I have no doubt they will be fixed in upcoming releases. And since I apparently have an SVN version thats why there are issues.
Thanks for clearing that up for me =)