There appears to be some issues with Cronjobs. This is being looked into now, and should be fixed soon. All coins that you have or will mine should be accounted for once this is fixed.
fixing a cronjob is less than 2 minutes work... I hope that they really didnt say that this way the issue.
If the default cron isn't working; manual crons can be triggered to at least have payouts made.
If shares are accounted for in the database; and blocks are registered in the pool; that means that cronjobs are working... Without a cronjob the shares aren't added into the database...
edit: apparently its fixed