Fixed in 2.0.2, which is live on itch now - update through the app or re-download from your library.
You were right that it was the same fault on both MP4 and WAV. Pace renders each kept section separately and joins them, and the fades on each section were being timed against the original clip's timeline rather than the section's own - so every section that didn't start at 00:00 was faded to silence before it began. One cut always worked because a single section skips the join, which is why this went unnoticed for so long.
There's now an automated test that exports three sections and fails if any come back silent, so it can't quietly return.
Thanks again for the detail in your report - it's what made this findable. The refund offer still stands if you'd rather not carry on, but I'd appreciate knowing whether 2.0.2 sorts it for you.