I’m having this same problem. My folder has 240 PNG images. At first, they were named 0001.png, 0002.png, etc. then I tried changing that to: character_ball_001.png, etc.
All 240 images make it into the viewer and from there, onto the timeline. But outputting from either the timeline or the playlist, only 229 images are converted into frames in the video output.
So, other than naming conventions, do you have any other suggestions?