Most likely you try to run a php script with the php binary directly which can not work in a jailed cronjob as the php binary is outside of the jail. Instead of using the php binary, insert just the url to the script in the command field of the cronjob in ispconfig like this:
ISPConfig will then take care that the script under that url is executed at the scheduled times.
Ok, thanks. I'll try in some hours. But... other question: why in other panels, like cPanel and Plesk this "problem" isn't present and scheduled backups via the wp-db backup plugn works perfectly?