The conductor was right. You had a rogue steward who made up his own rules. As a sleeper passenger, you're entitled to whatever diner meals happen to be available while you're aboard. If the train runs late and you're still on the train into an unexpected meal period, that's complimentary. By the same token, if the train is late before you board and you miss an expected meal period, it's usually tough luck. (Sometimes you can get comped items from the lounge if you ask nicely.)
Glad to hear that Customer Relations took care of you. Sounds like there are still some NYP-based crews who run things as personal fiefdoms and not for the benefit of their pax.