Your using define('DEVSYSTEM',1) in config.inc.php in ~/server/lib/config.inc.php right? Check your permissions as well and the /var/log/ispconfig/cron.log, could be that server.sh and cron_dailly.sh doesn't have the correct permissions (thats happened a couple times with me, had to change the permissions back). Oh, and check the permissions in the repo directory since its symbolically linked.
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-- RLB
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