Hi,
Thank you very much for the details, I was able to find the issue and probably fix it as well.
So due to the relatively large number of keywords, the plugin tries to assume the “pool size”, which is used when matching overlapping sets of results. When the pool size is too small, then potentially some of the results might be missed from the final list.
I have adjusted the pool sizes manually according to the keywords count, it should give you much better results now: https://i.imgur.com/o90UAgT.png
I hope this helps!