Ok I did what you said and created a shell script (/usr/local/ispconfig/server/test.sh) which has the following lines in it:
/usr/bin/php -q /usr/local/ispconfig/server/test.php
I then created test.php and put the same thing as the other php file I created (pinging google with the exec command).
I then ran test.sh as both root and as user ispconfig and it completed successfully for both. Do I need to run the script as a different user? What user do the cron jobs run under? All the files are owned by ispconfig user.