ISPConfig3 Lists no server and does not write changes.

[LordJason]

I've been searching the net all day, and I paid for the howtoforge subscription to download the documentation for ispconfig, and couldn't find an answer in there either. The closest thing I could find was this old thread. It pretty much sums up my problem, but was posted in 2005 for ISPConfig 2.

I followed the - perfect guide for debian-squeeze-with-bind-and-dovecot.

However a good portion of the guide was skipped (OS installation) as this is simply a Debian image provided by my vps host. Debian 6 64bit
2.6.32-194.26.1.el5.028stab081.1 x86_64 GNU/Linux

There were no errors during the installation.
I have enabled debugging via modifying the /usr/local/ispconfig/server/lib/config.inc.php file. (It wasn't possible to enable it through the web UI due to no server showing up in the list to configure)

Scrolling through the logfile I see a lot of:

09.01.2012-22:16 - DEBUG - Found 11 changes, starting update process.
09.01.2012-22:16 - DEBUG - Processed datalog_id 1
09.01.2012-22:16 - DEBUG - Processed datalog_id 2
09.01.2012-22:16 - DEBUG - Processed datalog_id 3
09.01.2012-22:16 - DEBUG - Processed datalog_id 4
09.01.2012-22:16 - DEBUG - Processed datalog_id 5
09.01.2012-22:16 - DEBUG - Processed datalog_id 6
09.01.2012-22:16 - DEBUG - Processed datalog_id 7
09.01.2012-22:16 - DEBUG - Processed datalog_id 8
09.01.2012-22:16 - DEBUG - Processed datalog_id 9
09.01.2012-22:16 - DEBUG - Processed datalog_id 10
09.01.2012-22:16 - DEBUG - Processed datalog_id 11
09.01.2012-22:16 - DEBUG - Remove Lock: /usr/local/ispconfig/server/temp/.ispconfig_lock

Then, I'm assuming when I tried to add a domain, we have

09.01.2012-22:21 - DEBUG - Calling function 'ssl' from plugin 'apache2_plugin' raised by event 'web_domain_insert'.
09.01.2012-22:21 - DEBUG - Calling function 'insert' from plugin 'apache2_plugin' raised by event 'web_domain_insert'.
09.01.2012-22:21 - WARNING - document_root not set
09.01.2012-22:21 - DEBUG - Processed datalog_id 12

The other two warnings that are repeated in the file:

09.01.2012-22:22 - WARNING - Skipping insertion of user:******, parent user web1 does not exist.
09.01.2012-22:22 - WARNING - Jailkit Plugin -> insert username:****** skipped, the user does not exist.

The page header has this:

Notice: Undefined offset: 0 in /usr/local/ispconfig/interface/web/monitor/lib/module.conf.php on line 63 Notice: Undefined offset: 0 in /usr/local/ispconfig/interface/web/monitor/lib/module.conf.php on line 64

Of course all of these are probably caused by the primary problem.
I checked the 'server' table, (there is no isp_server table) and it has zero records.

I should add that I already had some bind records and vhosts setup on this system before installing ispconfig. It's a simple sites-available links to sites-enabled setup. All of the current vhosts (only 3 at the moment) are simple named hosts. My vps only has two IP's at the moment. The nameserver, is setup with ns1.mydomain.com and ns2.mydomain.com pointing to each ip, and then each actual domains simply have an A record pointing to the first IP.
I also have Webmin running but I don't see how that should be a problem.

I just don't know what to check next.
Thank you for taking the time to read this.

EDIT: one more thing, I do have a php prepend script that simply fixes the value of DOCUMENT_ROOT. Considering ISPConfig is all php, I figured this may be somewhat relevant.