Hi Alex, thanks a lot for the quick response. Your explanation perfectly fits our situation. I updated the firmeware right before programming all the AudioMoths, so the batteries would already have been inserted and there would not have been a reset. And I just checked and the update was indeed to 1.2.1 from some previous version. It is possible/likely that the newer version AudioMoth (1.1.0) were already on that firmeware and I did not update those, hence they had no issues. We also noticed that the recording time was correct and assumed that that was controlled by the oscillator, thanks for confirming that too.
It's great to have your explanation, as we have been scratching our heads trying to figure out how this could have happened, but I am also glad to know that is is not a hardware issue and we won't have any problems with these devices going forward. We will make sure to run future firmware updates without batteries.
Best,
Mathias