I have the exact same problem with very short clips but even more strange.
I was recording with separate audio channels, one for the internal mic and one for a wireless lavalier. If I reboot I can listen to both, if I don’t I only listen to the internal mic of the camera. What’s funny about it is that I changed both audio channels to the left channel ( the one that had the lavalier) in the timeline, so I should only be listening to the lavalier instead of the internal mic.