Now I just truncate this script to "die();" because it fills all the memory with it's instances.
Thats not a good idea as we can not debug it like this. Remove the die command and comment it out in the root crontab instead.
Please enable debugging in the file /usr/local/ispconfig/server/lib/config,inc.php by setting the $conf["log_priority"] to 0 and then post the debug output that you get when you run:
rm -f /usr/local/ispconfig/server/temp/.ispconfig_lock