I think your hypothesis is strong.

I have noticed that during alignment it switches filter sometimes. Sometimes before alignement, sometimes after, sometimes it focuses the "previous target" filter sometimes the Lum filter.

I think I found one reproductible case: Right after meridian flip is completed, it will do an alignment, followed by one focus on Lum and then a focus on target filter.
Another case I saw, when it doesn't manage to do focus, it seems to revert to focusing Lum filter at some point.

Perhaps this together with a concurrency lock could cause the issue I have.

I went through a few analysis files and could find one, with filter changing behavior: