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Since you have moved on to a newer version of the DNG converter, I'm afraid this will have to be considered an isolated case.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.
Sorry, but I need to bring this one back from the dead.
Shooting the x100f with the Arcos film simulation, but shooting RAW+Fine as is my usual standard, so that I can pull out the color images if I want to. I'm still using Photoshop CS6, so I run my .raf files through Adobe DNG Converter (vers 18.104.22.1684) and keep both the originals and the new dng files. But when I open the dng with Photoshop Camera Raw I get the the RAW processing window with a black and white image - the Arcos Simulation, rather than the true RAW file.
If I use Alien Skins Exposure X3 to process the raw file I'm getting the color image, so there's something in the dng converter that's not working right, and bringing the film simulation along for the ride. I've got workarounds, but they're super clunky. It's a weird problem...
Sorry, I don't have an answer for you. I haven't had a Fuji camera for a long time. Haven't used the DNG converter much either. Suggest that you ask the question on a different forum where the developers monitor more closely. This is a user to user forum. Here is the link where you might get better help:
did you solve the issue? I get the same today with my Xt20 files.