Just to confirm, have you checked our Help Center article for managing comment notifications: https://goo.gl/CKNRJA ? Let us know if that helps.
Sorry to hear you're still having trouble. We'd recommend sending a feedback report directly from YouTube, here's how: https://goo.gl/WdI0BK . Make sure to send from the account experiencing the issue. We do review feedback and use the details to investigate and fix issues.