Actually, that was a feature, there's specifically something in the code to prevent the chemistry to work on command missions.
I don't know if it changed, but I was always convinced that it could not trigger from these missions. Time to change that. I'll have a look when I have a few minutes, I don't think that's something that is hard to fix.
Edit: I just released a fix for this. If you happen to face the situation again, please let me know if it's working as expected now.

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