I have a similar issue
I completed the Perfect Server Setup using SuSE 11.1 with no errors, I create a Client User, a Website, a Database and FTP user.
I uploaded the files by FTP with the user I create for it on ISPC3 and installed Joomla and all was fine until I try to change the joomla's global configuration.
A new conf file is generated and named "configuration.1 instead configuration.php I tried to chmod "configuration.php" but I get 550 error "Operation not permitted"
The site is running php cgi ssi fast-cgi+suExec
Thanks in advance for the help.