Ok, i've found something that might help. I've enabled query logging in MySQL and found the following:
203 Query SELECT * FROM sys_datalog WHERE datalog_id > 507 AND (server_id = 1 OR server_id = 0) ORDER BY datalog_id
204 Connect Access denied for user 'root'@'localhost' (using password: YES)
Is the cron job for creating the databases running with user root?