I have an issue opening some of my RAW format files from my Fuji XT-3. This only tends to happen with the XC 55-230mm lens at a maximum telephoto length. Some of the images it crops, others is makes a weird gradient after opening. When I delete the PP3 files, the preview goes back to normal. When I double click to open one, it does the weird gradient. Not all of my RAF files do this. It only happened recently with a handful of files. If I queue one without edit where it show fine in preview, the processing still leaves a gradient. I have Raw Therapee 5.3 installed under Ubuntu 18.01. The two screenshots show what it does in the app and 3 converted imaged from the same lens/set, but one at 55mm and two at 230mm focal length where the raf file has the issue. I am hoping someone may have some advise on this. I have also included one of my RAF files on here to test out._DSF3647.RAF (54.4 MB)
You should start by updating to the latest release, which is 5.7. There is a PPA, a flatpak, and an AppImage.
As suggested by @paperdigits , it works fine with latest 5.7 dev.