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Did you see in your application, in tab ALERTS if there is activated alert and check the actions , it can be email action somewhere?
though cron running as root, the script used for running log rotation script might be running as other user(non root). /var/log usually owned by root.
I have my own VM running locally, have two users root, lkoppolu. With lkoppolu I cant even access /var/log. change permissions for the user. It will work