You might need to speak with Sukrat (they should be by the jump sector), otherwise press F3, type in "stuff is broken", open the status menu missions section and shift click the mission's name.
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Much appreciated! But I found the reason - somehow I had two installs on my computer, one was 2.4.5 or so and then the newer 0.0.0 version... I removed the former and began a new run on the latter.
I have no idea how things ended up so mixed up, but in case things get bugged out again I will use your solution. Much appreciated!