Just want to share some of my experience.
I recently install my VPS with ISPConfig 3 on CentOS 5.5, it is similar to what u r doing. I also don't know the default install of the server. But I managed to run it with the help of people on this forum.
1. Are you sure you are using CentOS 5.5 64 bit? Because mine is 32 bit. If yours is 32 bit, then you must replace all file name containing x86_64 with i386.
2. If you're doing remove and reinstall of ISPConfig 3, don't forget to delete the dbispconfig in mysql after uninstall procedure. And also reboot after that. Because if not, the installer will say old database still exist and cannot continue.
3. Just to make sure we use the same way to install, I follow the guide from step 7-Install some software, there's no need to follow step 1-6 unless you have specific needs.
4. The only thing that was not installed on my default server is cron. If yours is the same, just do yum install vixie-cron
Ok, that's it from me. If still no result, you can view the install log to find the error.