Sweet! Many thanks. You literally just did my job for me. Will fix it right nowI just took a look inside and it's indeed just a dumb mistake.
It's around line 6009 of 004_global.js, in the extractSaveContents function (which is responsible for loading the save data).
The researches are set by a for loop, which starts at 1 instead of 0, skipping the negotiation skill in slot 0 (so it's not set and stay at 0 when you load a save file).
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I just wanted to make a patch but now I'm starting to think I may have to add some sort of readme listing out the people who contributed to this