I would question whether the DNG converter but actually do this on its own. All the DNG converter does is convert the data and put the raw image data in a new file container. I suspect that when you opened the images in what ever software you used you inadvertently applied some sort of preset that caused this to happen. Stranger things have happened to me.
I can't imagine how DNG would do it either, but I opened those files in LR, PS, and a simple image viewer called Xee, and all of them showed the same image; I also converted the most recent images along with the existing files on the card in different batches and opened them in different orders with those same viewers, and everything came out the same.
I would imagine the bug affected the DNG container; perhaps Fuji raw containers store some information about their film simulations or JPG processing, and DNG scrambled it. I know when I load a Fuji DNG into LR (I have LR 5, which does not support XT2 RAF files natively) it gives me the option of applying the film simulations. My guess is wherever that information comes from fueled the bug in the converter. Also, when I opened the develop module in LR, Acros was the only profile available, which I think would not be the case if LR applied a preset. It's not the camera either, because the DNG applied the same bug to old RAFs that had already been converted normally.
Since you have moved on to a newer version of the DNG converter, I'm afraid this will have to be considered an isolated case. Nobody else has reported this same problem that I am aware of. If you want to reinstall that version of the DNG converter and try to replicate the issue that would be one thing. However, since you are using the newer converter and are not seeing the problem I don't think this is an issue worth pursuing.