ISPConfig has a better mode then suphp which was not available in ispconfig 2 which also allows your sites to run under different users but its much faster. The recommended php mode in ispconfig 3 is:
PHP mode: fast-cgi
If you prefer to use the slower suphp kode, then you should first check under which user php is really run. You can do that with a script like this:
upload it to a website directory and open it in a browser. You will either get a error message that the file test.php could not be written to the directory were the php file is, this indicates that suphp is really not working. If you dont get a error message, then a test.txt file must have been created in the same directory, check on the shell or with a ftp client which user owns this file, is it www-data or is it the user of the website.