What does Yamaha say about this when you contact them?
If you haven't done so, this should be your first step. Let them know you have other files such as MP3 and FLAC which are in similar folders on the same drive which you can play back without issue, but you can't play these back.
I can't tell you how many features that never come to reality I have seen over the years, and this could easily be one of them. Or, you need to upgrade firmware, or your most recent firmware upgrade took that feature away.
But, definitely reach out to Yamaha, because they should have the best answer. Key word: SHOULD
Good luck!