I’ve recorded video that demonstrates the issue.
I run the same prerecorded audio clip through MB plugin to exclude any human error introduced by the live playing.
You can see the following in the video:
Project is fine, patch is saved, tracking works.
I reopen the project - patch name is lost, MIDI tracking becomes mangled until I tweak a noise gate again by the smallest margin, or reload patch manually.
Also you can notice another bug, that I cannot save patch under the name I had already used in previous sessions.