This very much sounds and matches the version for a similar bug I had/have and is also still not fixed.
I did not have more time (nor desire) to investigate. Ended-up using the latest working version (5.0.0-beta11).
I had the feeling it could be related to the materials upon merge. I eventually managed to fix some of the issues by changing the order of merged meshes according to whether they were using a single or multimat. But then, eventually, on another use case with no multimats, I got the same bug. Something, just something must have gone wrong with this update done (if I recall properly) after February 26.
I posted in this post which is I believe somehow related: